JP2013078311A - RNA INTERFERENCE MEDIATED INHIBITION OF HEPATITIS C VIRUS (HCV) GENE EXPRESSION USING SHORT INTERFERING NUCLEIC ACID (siNA) - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide methods and reagents useful in modulating hepatitis C virus (HCV) gene expression in a variety of applications, including use in therapeutic, diagnostic, target validation, and genomic discovery applications.SOLUTION: The invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against hepatitis C virus (HCV) gene expression and/or activity. The small nucleic acid molecules are useful in the treatment of HCV infection, liver failure, hepatocellular carcinoma, cirrhosis and any other disease or condition that responds to modulation of HCV expression or activity.

Description

  The present invention is disclosed in McSiggen, PCT / US02 / 09187 (filed March 26, 2002), U.S. Patent Application 60 / 401,104 (filed Aug. 5, 2002), Beigelman, U.S. Patent Application 60 / 358,580 ( Filed February 20, 2002), Beigelman, US patent application 60 / 363,124 (filed March 11, 2002), Beigelman, US patent application 60 / 386,782 (filed June 6, 2002), Beigelman US patent application 60 / 406,784 (filed 29 August 2002), Beigelman, US patent application 60 / 408,378 (filed 5 September 2002), Beigelman, US patent application 60 / 409,293 (2002) Filed September 9, 2010), and Beigelman, US patent Claims priority based on the gun 60 / 440,129 (January 15, 2003 application). These applications are hereby incorporated by reference in their entirety, including any drawings.

  The present invention relates to compounds, compositions, and methods for the study, diagnosis, and treatment of health conditions and diseases that respond to modulation of hepatitis C virus (HCV) gene expression and / or activity. The present invention also relates to compounds, compositions, and methods related to health conditions and diseases that respond to modulation of expression and / or activity of genes involved in the HCV pathway. In particular, the present invention relates to small nucleic acid molecules capable of mediating RNA interference (RNAi) against gene expression of hepatitis C virus (HCV), such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double stranded RNA ( dsRNA), microRNA (miRNA), and short hairpin RNA (shRNA) molecules.

  The following is a description of related technologies related to RNAi. This description is provided only for the understanding of the invention described below. This summary is not an admission that any of the work described below is prior art to the present invention.

  RNA interference refers to the process of sequence-specific post-transcriptional gene silencing mediated by short interfering RNA (siRNA) in animals (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and in fungi also referred to as querying. The post-transcriptional gene silencing process is thought to be an evolutionarily conserved cellular defense mechanism used to prevent the expression of foreign genes, and has different plexus and gates in common ( Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression is achieved by homologous single-stranded RNA or viral genomic RNA in response to the generation of double-stranded RNA (dsRNA) resulting from viral infection or random integration of transposon elements into the host genome. It may have evolved by a cellular response that specifically destroys. The presence of dsRNA in cells triggers an RNAi response by a mechanism that has not yet been fully characterized. This mechanism appears to be different from the interferon response that results in non-specific cleavage of mRNA by ribonuclease L as a result of dsRNA-mediated activation of protein kinases PKR and 2 ', 5'-oligoadenylate synthetase.

The presence of long dsRNA in the cell stimulates the activity of a ribonuclease III enzyme called Dicer. Dicer is involved in processing dsRNA into short fragments of dsRNA known as short interfering RNA (siRNA) (Berste).
in et al. , 2001, Nature, 409, 363). Short interfering RNA resulting from Dicer activity is typically about 21-23 nucleotides in length and contains about 19 base pair duplexes (Elbashir et al., 2001, Genes Dev., 15, 188). Dicer has also been implicated in excising 21 and 22 nucleotide small transient RNAs (stRNAs) from conserved precursor RNAs implicated in translational control (Hutvagner et al.
al. , 2001, Science, 293,834). The RNAi response is also characterized by an endonuclease complex, commonly referred to as the RNA-induced silencing complex (RISC), which cleaves single-stranded RNA having a sequence complementary to the antisense strand of the siRNA duplex. Mediate. Cleavage of the target RNA occurs in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188).

  RNAi has been studied in various systems. Fire et al. (1998, Nature, 391, 806) is a C.I. RNAi was first observed in Elegans. Wianny and Goetz (1999, Nature Cell Biol., 2, 70) describe RNAi mediated by dsRNA in mouse embryos. Hammond et al. (2000, Nature, 404, 293) describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al. (2001, Nature, 411, 494) describe RNAi induced by introducing synthetic 21 nucleotide RNA duplexes in cultured mammalian cells such as human embryonic kidney cells and HeLa cells. Recent work in Drosophila embryo lysates (Elbashir et al., 2001, EMBO J, 20, 6877) has shown that siRNA length, structure, chemical composition, and sequence are essential to mediate efficient RNAi activity. Clarified certain requirements for. These studies showed that the 21 nucleotide siRNA duplex was most active when it contained a 3 'terminal dinucleotide overhang. Furthermore, replacement of one or both siRNA strands with 2′-deoxy (2′-H) or 2′-O-methyl nucleotides destroys RNAi activity, but 3 ′ terminal siRNA overhanging nucleotides are replaced with 2′-deoxy. It has been shown that substitution with nucleotides (2'-H) is permissible. A single mismatch sequence in the center of the siRNA duplex has also been shown to disrupt RNAi activity. In addition, these studies also showed that the position of the cleavage site in the target RNA is defined by the 5 ′ end of the guide sequence rather than the 3 ′ end of the siRNA guide sequence (Elbashir et al., 2001, EMBO J. et al. , 20, 6877). Other studies have shown that the 5'-phosphate of the target complement of the siRNA duplex is required for siRNA activity and that ATP is used to maintain the 5'-phosphate component of the siRNA (Nykanen et al , 2001, Cell, 107, 309).

It has been shown that replacing the overhanging segment of the 3 'terminal nucleotide of a 21-mer siRNA duplex with a 2 nucleotide 3'-overhang with deoxyribonucleotides has no detrimental effect on RNAi activity. Yes. Although it has been reported that replacing up to 4 nucleotides at each end of siRNA with deoxyribonucleotides is well tolerated, complete substitution with deoxyribonucleotides eliminates RNAi activity (Elbashir et al., 2001, EMBO J. et al. , 20, 6877). In addition, Elbashir et al. (Supra) also report that substitution of siRNA with 2'-O-methyl nucleotides completely abolished RNAi activity. Li et al. (International Publication WO 00/44914) and Beach et al. (International Publication WO 01/68836) can modify siRNA to include at least one of a nitrogen or sulfur heteroatom in either the phosphate-sugar backbone or the nucleoside. Preliminarily suggest what you can do. However, neither application assumes how much such modifications are allowed in siRNA molecules and provides no further guidance or examples of such modified siRNAs. Kreutzer et al. (Canadian patent application 2,359,180) also describes certain chemical modifications for use in the dsRNA constructs to prevent activation of the double-stranded RNA-dependent protein kinase PKR, particularly 2'-amino or 2'-O-methyl nucleotides and nucleotides containing 2'-O or 4'-C methylene bridges are described. However, Kreutzer et al. Similarly does not provide examples or guidance on how much of these modifications are allowed in siRNA molecules.

  Parrish et al. (2000, Molecular Cell, 6, 1977-1087). Certain chemical modifications targeting the unc-22 gene were tested with long (> 25 nt) siRNA transcripts in elegans. The authors introduced thiophosphate residues in these siRNA transcripts by incorporating thiophosphate nucleotide analogs with T7 and T3 RNA polymerases, and RNAs with two phosphorothioate modified bases are also effective as RNAi It describes that the sex was substantially reduced. In addition, Parrish et al. Report that phosphorothioate modifications with more than two residues destabilized RNA in vitro such that interfering activity could not be assayed (Id., 1081). The authors also tested for certain modifications at the 2 'position of the nucleotide sugar in long siRNA transcripts, replacing ribonucleotides with deoxynucleotides, particularly uridine to thymidine and / or cytidine to deoxycytidine. In the case of, the interference activity was found to decrease substantially (Id.). In addition, the authors have made certain base modifications, such as 4-thiouracil, 5-bromouracil, 5-iodouracil, and 3- (aminoallyl) uracil instead of uracil in the sense and antisense strands of siRNA, And substitution of inosine instead of guanine was tested. Although 4-thiouracil and 5-bromouracil substitutions seemed to be tolerated, Parrish reports that inosine produced a substantial reduction in interfering activity when incorporated into either strand. . Parrish also reports that the incorporation of 5-iodouracil and 3- (aminoallyl) uracil in the antisense strand also substantially reduced RNAi activity.

The use of longer dsRNA has been described. For example, Beach et al. (International Publication No. WO 01/68836) describe specific methods for attenuating gene expression using endogenous dsRNA. Tuschl et al. (International Publication WO 01/75164) describe the Drosophila in vitro RNAi system and the use of specific siRNA molecules for certain functional genomic applications and certain therapeutic applications. However, Tuschl (2001, Chem. Biochem., 2, 239-245) is suspicious that RNAi can be used to cure genetic diseases or viral infections due to the risk of activating the interferon response. Says. Li et al. (International Publication WO 00/44914) describe the use of specific dsRNAs to attenuate the expression of certain target genes. Zernika-Goetz et al. (International Publication No. WO 01/36646) describe certain methods of inhibiting the expression of specific genes in mammalian cells using certain dsRNA molecules. Fire et al. (International Publication No. WO 99/32619) describe special methods for introducing certain dsRNA molecules into cells for use in inhibiting gene expression. Plaetinck et al. (International Publication No. WO 00/01846) describe certain methods for identifying specific genes responsible for conferring a particular phenotype in cells using specific dsRNA molecules. Melo et al. (International Publication WO 01/29058) describe the identification of specific genes involved in dsRNA-mediated RNAi. Deschamps Depallette et al. (International Publication No. WO 99/07409) describe specific compositions consisting of special dsRNA molecules in combination with certain antiviral agents. Waterhouse et al. (WO 99/53050) describe certain methods of reducing nucleic acid phenotype expression in plant cells using certain dsRNAs. Driscoll et al. (International Publication WO 01/49844)
A specific DNA construct for use in promoting gene silencing in a target organism is described.

  Others have reported various RNAi and gene silencing systems. For example, Parrish et al. (2000, Molecular Cell, 6, 1977-1087) A specific chemically modified siRNA construct targeting the elegans unc-22 gene is described. Grossnikulaus (WO 01/38551) describes certain methods for controlling polycomb gene expression using certain dsRNAs in plants. Churikov et al. (International Publication No. WO 01/42443) describe certain methods of modifying the genetic properties of an organism using certain dsRNAs. Cogoni et al. (International Publication No. WO 01/53475) describe certain methods of isolating Neurospora silencing genes and their uses. Reed et al. (International Publication No. WO 01/68836) describe certain methods of gene silencing in plants. Honer et al. (International Publication WO 01/70944) describe certain methods of drug screening using transgenic nematodes as a model of Parkinson's disease using certain dsRNAs. Deak et al. (International Publication No. WO 01/72774) describe certain Drosophila-derived gene products that may be related to RNAi in Drosophila. Arndt et al. (International Publication No. WO 01/92513) describe certain methods of mediating gene suppression using factors that enhance RNAi. Tuschl et al. (International Publication WO 02/44321) describe certain synthetic siRNA constructs. Pachuk et al. (International Publication WO 00/63364) and Satishchanran et al. (International Publication WO 01/04313) describe certain methods and compositions for inhibiting the function of certain polynucleotide sequences using certain dsRNAs. To do. Echeverri et al. (International Publication No. WO 02/38805) has reported that certain C. cerevisiae identified by RNAi. The elegans gene is described. Kreutzer et al. (International Publications WO02 / 055692, WO02 / 055693, and EP1144623B1) describe certain methods of inhibiting gene expression using RNAi. Graham et al. (International Publications WO99 / 49029 and WO01 / 70949, and AU4037501) describe certain siRNA molecules that are expressed from vectors. Fire et al. (US 6,506,559) describe certain methods for inhibiting gene expression in vitro using RNAi-mediated lengths of dsRNA (greater than 25 nucleotides).

  McCaffrey et al. (2002, Nature, 418, 38-39) describe the use of certain siRNA constructs that target chimeric HCV NS5B protein / luciferase transcripts in mice.

  Randall et al. (2003, PNAS USA, 100, 235-240) describe certain siRNA constructs that target HCV RNA in the Huh7 liver cancer cell line.

SUMMARY OF THE INVENTION The present invention relates to genes such as HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, and / or other diseases associated with HCV infection by RNA interference (RNAi) using short interfering nucleic acid (siNA) molecules. It relates to compounds, compositions and methods useful for modulating the expression of genes associated with the development or maintenance of the condition. The present invention also uses small nucleic acid molecules, such as short interfering nucleic acids (siNA), short interfering RNA (siRNA), double stranded RNA (dsRNA), microRNA (miRNA), and short hairpin RNA (shRNA) molecules. , RNA interference (RNAi), expression and activity of hepatitis C virus (HCV), or hepatitis C virus (HC
V) relates to compounds, compositions and methods useful for regulating genes involved in gene expression and / or activity. In particular, the present invention relates to small nucleic acid molecules used to regulate the expression of hepatitis C virus (HCV), such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double stranded RNA (dsRNA), Features microRNA (miRNA), and short hairpin RNA (shRNA) molecules and methods. The siNA of the present invention may not be modified but may be chemically modified. The siNA of the present invention may be chemically synthesized, expressed from a vector, or enzymatically synthesized. The invention also features a variety of chemically modified synthetic short interfering nucleic acid (siNA) molecules that can modulate the expression or activity of hepatitis C virus gene in cells by RNA interference (RNAi). By using chemically modified siNA, various properties of native siNA molecules are improved for increased resistance to nuclease degradation in vivo and / or improved cellular uptake. Furthermore, contrary to earlier published work, siNA with many chemical modifications retains its RNAi activity. The siNA molecules of the present invention provide reagents and methods useful for various therapeutic, diagnostic, target assessment, genome discovery, genetic engineering, and pharmacogenomic applications.

  In one aspect, the invention features one or more siNA molecules and methods that modulate the expression of a gene encoding hepatitis C virus, independently or in combination. Specifically, the invention features siNA molecules that regulate the expression of HCV proteins, eg, proteins encoded by the Genbank accession number sequences shown in Table I.

  In one aspect, the invention relates to an HCV negative chain, such as Genbank accession number HPCK1S1, hepatitis C virus (HCV-1b strain, clone HCV-K1-S1), complete genome; Genbank accession number D50483; 9410 nt. Characterized by siNA molecules with RNAi specificity.

  In one embodiment, the present invention, independently or in combination, provides cell targets for HCV infection, such as cell receptors, cell surface molecules, cell enzymes, cell transcription factors, and / or cytokines, second messengers, and cell accessories. Molecules, such as, but not limited to, interferon regulators (IRFs; eg Genbank accession number AF082503.1); cellular PKR protein kinases (eg Genbank accession number XM — 002661.7); human eukaryotic initiation factor 2B (elF2B gamma; For example, Genbank accession number AF256223 and / or elF2 gamma; eg, Genbank accession number NM — 006874.1); human DEAD box protein (DDX3; eg, Genbank accession number XM — 18021.2); and regulates the expression of genes for cellular proteins that bind to the poly (U) tract of HCV 3′-UTR, such as polypyrimidine tract binding proteins (eg Genbank accession numbers NM — 031991.1 and XM — 04292.3) Or more siNA molecules and methods.

Due to the high sequence variability of the HCV genome, the selection of siNA molecules for broad therapeutic applications will include conserved regions of the HCV genome. In one aspect, the invention relates to siNA molecules that target conserved regions of the HCV genome. Examples of conserved regions of the HCV genome include, but are not limited to, 5′-noncoding regions (NCR, 5′-nontranscribed regions, also referred to as UTRs), 5 ′ ends of core protein coding regions, and 3′- NCR is included. HCV genomic RNA contains an internal ribosome entry site (IRES) in the 5′-NCR, which mediates translation independent of the 5′-cap structure (Wang et al., 1993, J. Virol., 67). 3338-44). The full length sequence of the HCV RNA genome varies among clinically isolated subtypes, of which there are at least 15 (Simmonds, 1995, Hepatology, 21, 570-583), but HCV 5'- NCR sequences are highly conserved among all known subtypes, probably because they conserve a common IRES mechanism (Okamoto et al., 1991, J. General Virol., 72). 2697-2704). Thus, siNA molecules can be designed to target all of the different isolates of HCV. SiNA molecules designed to target conserved regions of various HCV isolates enable effective inhibition of HCV replication in various patient populations and evolve HCV pseudospecies by mutations in non-conserved regions of the HCV genome The effectiveness of siNA molecules against can be assured. Thus, by designing siNA molecules to interact with conserved nucleotide sequences of HCV, one siNA molecule can be targeted to all isolates of HCV (all such conserved sequences are Present in the RNA of HCV isolates).

  In one embodiment, the present invention independently or in combination comprises a gene encoding a cellular protein associated with the maintenance or development of HCV and / or HCV infection, liver failure, hepatocellular carcinoma, and cirrhosis, eg, a table Features one or more siNA molecules and methods that modulate the expression of a gene encoding the sequence represented by the GenBank accession number shown in I (commonly referred to herein as HCV). In the following, various aspects and embodiments of the invention will be described with reference to an exemplary hepatitis C virus (HCV) gene (generally referred to herein as HCV). However, such reference is meant to be exemplary only, and the various aspects and embodiments of the present invention also include other HCV genes such as mutant HCV genes, spliced variants of HCV genes, and genes encoding HCV of different strains, As well as other genes that express cellular targets of HCV, such as those described herein. Various aspects and embodiments also include other genes involved in the HCV pathway, such as genes encoding cellular proteins involved in the maintenance and / or development of HCV infection, liver failure, hepatocellular carcinoma, and cirrhosis, or HCV infection It is also directed to other genes that express other proteins related to C, such as cellular proteins utilized in the life cycle of HCV. Such additional genes can be analyzed for target sites using the methods described herein for HCV. That is, inhibition of other genes and the effects of such inhibition can be performed as described herein. In other words, the term “HCV” referred to in the embodiments defined and described below encodes a gene associated with the development or maintenance of HCV infection, eg, an HCV polypeptide such as a polypeptide of a different strain of HCV. Gene, mutant HCV gene, and spliced variant of HCV gene, as well as cellular genes involved in the HCV pathway of gene expression, replication, and / or HCV activity. Also, the term “HCV” referred to in the embodiments defined and described below includes HCV viral gene products and cellular gene products involved in HCV infection, such as those described herein. means. That is, each embodiment described herein with reference to the term “HCV” refers to all viruses covered by the term “HCV”, as that term is defined herein. , Applicable to cellular and viral proteins, peptides, polypeptides, and / or polynucleotide molecules.

  In one aspect, the invention features a siNA molecule that down regulates expression of an HCV gene, eg, the HCV gene comprises an HCV coding sequence.

  In one aspect, the invention features a siNA molecule having RNAi activity against HCV RNA, wherein the siNA molecule is a sequence complementary to any RNA having HCV or other sequences encoded by HCV, such as Table I The sequence having the GenBank accession number shown in FIG. The chemical modifications shown in Tables III and IV or herein can be applied to any siNA construct of the present invention.

In one embodiment, the present invention provides si having RNAi activity against HCV RNA.
Characterized by an NA molecule, the siNA molecule comprises a sequence complementary to any RNA having an HCV coding sequence, eg, a sequence having the HCV GenBank accession number shown in Table I. The chemical modifications shown in Tables III and IV or herein can be applied to any siNA construct of the invention.

  In another aspect, the invention features a siNA molecule having RNAi activity against an HCV gene, wherein the siNA molecule is a nucleotide sequence complementary to a nucleotide sequence of an HCV gene, eg, an HCV sequence having a GenBank accession number shown in Table I including. In another embodiment, the siNA molecule of the invention comprises a nucleotide sequence that can interact with the nucleotide sequence of the HCV gene to mediate silencing of HCV gene expression, eg, siNA is a chromatin structure of the HCV gene. It mediates the regulation of HCV gene expression by a cellular process that alters and prevents transcription of the HCV gene.

  In another aspect, the invention features a siNA molecule that includes a nucleotide sequence in the antisense region of the siNA molecule, eg, a nucleotide sequence complementary to a nucleotide sequence or a portion of a sequence of an HCV gene. In another aspect, the invention features a siNA molecule that includes a region that is complementary to a sequence or portion of a sequence that includes an HCV gene sequence, eg, an antisense region of a siNA construct.

  In one embodiment, the antisense region of the HCV siNA construct can comprise a sequence that is complementary to a sequence having either SEQ ID NO: 1-696 or 1393-1413. In one embodiment, the antisense region also has SEQ ID NOs: 697-1392, 1414, 1420, 1428-1434, 1456-1462, 1479, 1483, 1489-1491, 1497-1498, 1500, 1513-1524. 1551, 1556, 1570-1581, 1618, 1620, 1622, 1624, 1626, or 1627 may be included. In another embodiment, the sense region of the HCV construct is SEQ ID NO: 1-696, 1393-1413, 1417-1419, 1421-1427, 1449-1455, 1477, 1481, 1485, 1487, 1494-1496, 1499, 1501. -1512, 1549, 1553, 1558-1569, 1582-1593, 1617, 1619, 1621, 1623, or 1625 can be included. The sense region can include the sequence of SEQ ID NO: 1606, and the antisense region can include the sequence of SEQ ID NO: 1607. The sense region can include the sequence of SEQ ID NO: 1608 and the antisense region can include the sequence of SEQ ID NO: 1609. The sense region can include the sequence of SEQ ID NO: 1610, and the antisense region can include the sequence of SEQ ID NO: 1611. The sense region can include the sequence of SEQ ID NO: 1612 and the antisense region can include the sequence of SEQ ID NO: 1613. The sense region can include the sequence of SEQ ID NO: 1614, and the antisense region can include the sequence of SEQ ID NO: 1615. The sense region can include the sequence of SEQ ID NO: 1612 and the antisense region can include the sequence of SEQ ID NO: 1616.

  In one embodiment, the siNA molecule of the invention comprises any of SEQ ID NOs: 1-1627. The sequence shown in SEQ ID NO: 1-1627 is not limiting. The siNA molecule of the invention may comprise any contiguous HCV sequence (eg, about 19 to about 25, or about 19, 20, 21, 22, 23, 24, or 25 contiguous HCV nucleotides). it can.

In yet another aspect, the invention provides a sequence comprising a sequence represented by the GenBank accession number shown in Table I or a sequence complementary to a portion of the sequence, eg, an siNA molecule comprising an antisense sequence of a siNA construct. It is characterized by. The chemical modifications described in Tables III and IV and herein can be applied to any siRNA construct of the invention.

  In one embodiment of the invention, the siNA molecule comprises an antisense strand having from about 19 to about 29 nucleotides, the antisense strand is complementary to an RNA sequence encoding an HCV protein, and the siNA is further about 19 -Comprising a sense strand having about 29 (eg, about 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29) nucleotides, wherein the sense and antisense strands are at least about 19 complementary A separate nucleotide sequence with nucleotides.

  In another aspect of the invention, the siNA molecules of the invention have from about 19 to about 29 (eg, about 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29) nucleotides. An antisense region, wherein the antisense region is complementary to an RNA sequence encoding an HCV protein, the siNA further comprises a sense region having from about 19 to about 29 nucleotides, wherein the sense and antisense regions are at least about 19 Linear molecules having the complementary nucleotides of

  In one embodiment of the invention, the siNA molecule comprises an antisense strand comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding an HCV protein or a portion thereof. siNA further comprises a sense strand, which comprises the nucleotide sequence of the HCV gene or a portion thereof.

  In another embodiment, the siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding HCV protein or a portion thereof. The siNA molecule further includes a sense region, which includes the nucleotide sequence of the HCV gene or a portion thereof.

In one embodiment, the siNA molecule of the invention has RNAi activity that regulates the expression of RNA encoded by the HCV gene. Since HCV genes can share some sequence homology with each other, siNA molecules can share a group of HCV genes by selecting sequences that are shared between different HCV targets or unique to a particular HCV target. It can be targeted or designed to target a specific HCV gene. Thus, in one embodiment, a siNA molecule may target several HCV genes so that one siNA molecule targets several HCV genes (eg, different HCV isoforms, splicing variants, mutant genes, etc.). HCV with homology between
It can be designed to target conserved regions of RNA sequences. In another embodiment, siNA molecules can be designed to target sequences that are unique to a particular HCV RNA sequence because of the high degree of specificity that siNA molecules require to mediate RNAi activity.

  In one embodiment, the nucleic acid molecules of the invention that act as mediators of RNA interference gene silencing responses are double stranded nucleic acid molecules. In another embodiment, siNA molecules of the invention comprise about 19 base pairs between oligonucleotides comprising about 19 to about 25 (eg, about 19, 20, 21, 22, 23, 24 or 25) nucleotides. Consists of duplex. In yet another embodiment, the siNA molecule of the invention is a duplex having an overhang end of about 1 to about 3 (eg, about 1, 2, or 3) nucleotides, eg, about 19 base pairs and a 3 ′ terminal mononucleotide. , Dinucleotides, or about 21 nucleotide duplexes with trinucleotide overhangs.

In one aspect, the invention features one or more chemically modified siNA constructs having specificity for a nucleic acid molecule that expresses HCV, such as RNA encoding an HCV protein. Non-limiting examples of such chemical modifications include, but are not limited to, phosphorothioate internucleotide linkages, 2′-deoxyribonucleotides, 2′-O-methylribonucleotides, 2′-deoxy-2′-fluororibonucleotides, "
Incorporation of universal bases “nucleotides”, “acyclic” nucleotides, 5-C-methyl nucleotides, and terminal glyceryl and / or inverted deoxyabasic residues These chemical modifications are incorporated into various siNA constructs. When used, it has been shown to retain RNAi activity in cells and at the same time dramatically increase the serum stability of these compounds, contrary to the data published by Parrish et al. In the present invention, multiple (2 or more) phosphorothioate substitutions are well tolerated and are shown to substantially increase the serum stability of the modified siNA constructs.

  In one embodiment, the siNA molecules of the invention comprise modified nucleotides while maintaining the ability to mediate RNAi. Modified nucleotides can be used to improve in vitro or in vivo properties such as stability, activity, and / or bioavailability. For example, siNA molecules of the invention can include modified nucleotides as a percentage of the total number of nucleotides present in the siNA molecule. That is, siNA molecules of the invention generally have about 5% to about 100% modified nucleotides (eg, about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45 %, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% modified nucleotides). The actual percentage of modified nucleotides present in a given siNA molecule will depend on the total number of nucleotides present in the siNA. If the siNA molecule is single stranded, the percent modification can be based on the total number of nucleotides present in the single stranded siNA molecule. Similarly, if the siNA molecule is double stranded, the percent modification can be based on the total number of nucleotides present in the sense strand, antisense strand, or both the sense and antisense strands.

  In one aspect, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double-stranded siNA molecule is an HCV RNA An antisense strand comprising a nucleotide sequence complementary to the nucleotide sequence or a part thereof, and the other strand is a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand. In one embodiment, the HCV RNA comprises HCV negative strand RNA. In another embodiment, the HCV RNA comprises HCV plus strand RNA.

In one aspect, the invention features a double stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double stranded siNA molecule is a nucleotide of HCV RNA. An antisense strand comprising a nucleotide sequence complementary to the sequence or a part thereof, the other strand being a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, in a double stranded siNA molecule Most of the pyrimidine nucleotides present contain sugar modifications. In one embodiment, all pyrimidine nucleotides present in the double stranded siNA molecule contain a sugar modification. In one embodiment, each strand of the double stranded siNA molecule comprises about 19 to about 29 nucleotides, and each strand comprises at least about 19 nucleotides complementary to the nucleotides of the other strand. In another embodiment, the double stranded siNA molecule is assembled from two oligonucleotide fragments, one fragment comprising the nucleotide sequence of the antisense strand of the siNA molecule and the second fragment being the nucleotide sequence of the sense strand of the siNA molecule. including. In yet another embodiment, the sense strand of the double stranded siNA molecule is linked to the antisense strand via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker. In another embodiment, any pyrimidine nucleotide (ie, one or more or all) present in the sense strand of a double stranded siNA molecule is a 2′-deoxy-2′-fluoro pyrimidine nucleotide and is present in the sense region. Any purine nucleotide (ie, one or more or all) that is a 2′-deoxypurine nucleotide. In yet another embodiment, the sense strand of the double stranded siNA molecule comprises a 3 ′ end and a 5 ′ end and is end-capped at the 5 ′ end, 3 ′ end, or both the 5 ′ end and the 3 ′ end of the sense strand. There are components (eg, inverted deoxy abasic components). In another embodiment, the antisense strand of a double stranded siNA molecule comprises one or more 2′-deoxy-2′-fluoropyrimidine nucleotides and one or more 2′-O-methylpurine nucleotides. In yet another embodiment, any pyrimidine nucleotide present in the antisense strand of a double stranded siNA molecule is a 2′-deoxy-2′-fluoropyrimidine nucleotide and any purine nucleotide present in the antisense strand is 2 '-O-methylpurine nucleotide. In another embodiment, the antisense strand of the double stranded siNA molecule comprises a phosphorothioate internucleotide linkage at the 3 ′ end of the antisense strand. In yet another embodiment, the antisense strand comprises a glyceryl modification at the 3 ′ end of the antisense strand. In yet another embodiment, the 5 ′ end of the antisense strand may optionally contain a phosphate group.

  In one aspect, the invention features a double stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double stranded siNA molecule is a nucleotide of HCV RNA. An antisense strand comprising a nucleotide sequence complementary to the sequence or part thereof, the other strand being a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, present in a double stranded siNA molecule Most of the pyrimidine nucleotides contain sugar modifications, and each of the two strands of the siNA molecule contains 21 nucleotides. In one embodiment, the 21 nucleotides of the antisense strand are base paired with the nucleotide sequence of HCV RNA or a portion thereof. In another embodiment, about 19 nucleotides of the antisense strand are base-paired with the nucleotide sequence of HCV RNA or a portion thereof. In one embodiment, each strand of the siNA molecule base pairs with a complementary nucleotide in the other strand of the siNA molecule. In another embodiment, about 19 nucleotides of each strand of the siNA molecule are base-paired with complementary nucleotides of the other strand of the siNA molecule, and at least two 3 ′ terminal nucleotides of each strand of the siNA molecule are the other of the siNA molecule. It does not base pair with the other nucleotides. In one embodiment, each of the two non-base-paired 3 'terminal nucleotides of each strand of the siNA molecule is a 2'-deoxy-pyrimidine, such as 2'-deoxy-thymidine.

  In one aspect, the invention features a double stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double stranded siNA molecule is a nucleotide of HCV RNA. An antisense strand comprising a nucleotide sequence complementary to the sequence or part thereof, the other strand being a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, present in a double stranded siNA molecule Most of the pyrimidine nucleotides that contain a sugar modification are such that the nucleotide sequence of the antisense strand or part thereof is complementary to the nucleotide sequence of the 5′-untranslated region of HCV RNA or part thereof.

  In another aspect, the invention features a double stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double stranded siNA molecule is a nucleotide of HCV RNA. An antisense strand comprising a nucleotide sequence complementary to the sequence or part thereof, the other strand being a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, present in a double stranded siNA molecule The majority of pyrimidine nucleotides that contain a sugar modification, the nucleotide sequence of the antisense strand, or part thereof, is complementary to the nucleotide sequence of HCV RNA present in all HCV RNA.

In one aspect, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits replication of hepatitis C virus (HCV), wherein one strand of the double-stranded siNA molecule is an HCV protein or its An antisense strand comprising a nucleotide sequence complementary to the nucleotide sequence of RNA encoding the fragment, and the other strand is a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand. In one embodiment, the majority of pyrimidine nucleotides present in the double stranded siNA molecule contain sugar modifications.

  In one aspect, the invention features a pharmaceutical composition comprising a siNA molecule of the invention in an acceptable carrier or diluent.

  In one aspect, the invention features a pharmaceutical comprising the siNA molecule of the invention.

  In one aspect, the invention features an active ingredient that includes a siNA molecule of the invention.

  In one embodiment, the nucleotide sequence of the antisense strand of the siNA molecule of the invention or part thereof is complementary to the nucleotide sequence of HCV RNA or part thereof present in the RNA of all HCV isolates. .

  In one aspect, the invention features the use of a double stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double stranded siNA molecule is HCV An antisense strand comprising a nucleotide sequence complementary to the nucleotide sequence of RNA or a part thereof, and the other strand is a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, the double strand Most of the pyrimidine nucleotides present in the siNA molecule contain sugar modifications.

  In a non-limiting example, the introduction of chemically modified nucleotides into a nucleic acid molecule is a potential limitation of in vivo stability and bioavailability inherent in naturally delivered natural RNA molecules. Providing powerful tools to solve the problem. For example, chemically modified nucleic acid molecules tend to have a longer half-life in serum, so using chemically modified nucleic acid molecules can help to reduce the specific nucleic acid molecules required for a given therapeutic effect. The dose can be reduced. In addition, certain chemical modifications can improve the bioavailability of nucleic acid molecules by targeting specific cells or tissues and / or improving cellular uptake of the nucleic acid molecule. Thus, even if the activity of a chemically modified nucleic acid molecule is low compared to a natural nucleic acid molecule, for example when compared to a total RNA nucleic acid molecule, the improved stability and / or delivery of the molecule. Thus, the overall activity of the modified nucleic acid molecule may be higher than the natural molecule. Unlike natural unmodified siNA, chemically modified siNA can also minimize the possibility of activating interferon activity in humans.

  The antisense region of the siNA molecule of the present invention can include a phosphorothioate internucleotide linkage at the 3 'end of the antisense region. The antisense region can comprise about 1 to about 5 phosphorothioate internucleotide linkages at the 5 'end of the antisense region. The 3 'terminal nucleotide overhangs of the siNA molecules of the invention can include ribonucleotides or deoxyribonucleotides that are chemically modified with the sugar, base, or backbone of the nucleic acid. The 3 'terminal nucleotide overhang can comprise one or more universal base ribonucleotides. The 3 'terminal nucleotide overhang can comprise one or more acyclic nucleotides.

One aspect of the invention provides an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention in a manner that allows expression of the nucleic acid molecule. Another aspect of the present invention provides mammalian cells comprising such expression vectors. The mammalian cell may be a human cell. The siNA molecule of the expression vector can include a sense region and an antisense region. The antisense region can include a sequence complementary to the RNA or DNA sequence encoding HCV, and the sense region can include a sequence complementary to the antisense region. The siNA molecule can comprise two separate strands with complementary sense and antisense regions. The siNA molecule can comprise a single strand having complementary sense and antisense regions.

［式中，
各Ｒ１およびＲ２は，独立して，任意のヌクレオチド，非ヌクレオチド，またはポリヌクレオチドであり，これは天然に生ずるものであっても化学的に修飾されたものでもよく，各ＸおよびＹは，独立して，Ｏ，Ｓ，Ｎ，アルキル，または置換アルキルであり，各ＺおよびＷは，独立して，Ｏ，Ｓ，Ｎ，アルキル，置換アルキル，Ｏ−アルキル，Ｓ−アルキル，アルカリール，またはアラルキルであり，Ｗ，Ｘ，Ｙ，およびＺは任意に全てＯでなくてもよい］
を有する骨格修飾ヌクレオチド間結合を含む，１またはそれ以上（例えば，約１，２，３，４，５，６，７，８，９，１０個またはそれ以上）のヌクレオチドを含む。 In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, the chemical modification is represented by the formula I:

[Where,
Each R1 and R2 is independently any nucleotide, non-nucleotide, or polynucleotide, which may be naturally occurring or chemically modified, and each X and Y is independently O, S, N, alkyl, or substituted alkyl, and each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, or Aralkyl, and W, X, Y, and Z are not necessarily all O]
1 or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) nucleotides containing backbone modified internucleotide linkages having

  For example, any chemically modified internucleotide linkage having Formula I wherein any Z, W, X, and / or Y independently contains a sulfur atom is attached to one or both oligonucleotide strands of the siNA duplex, eg, It can be present on the sense strand, the antisense strand, or both strands. The siNA molecules of the present invention may have one or more (eg, about 1, 2 or 3) at the 3 ′ end, 5 ′ end, or both 3 ′ and 5 ′ ends of the sense strand, antisense strand, or both strands. , 3, 4, 5, 6, 7, 8, 9, 10 or more) may include chemically modified internucleotide linkages having Formula I. For example, exemplary siNA molecules of the invention have about 1 to about 5 or more (eg, about 1, 2, 3, 4, 5) at the 5 ′ end of the sense strand, antisense strand, or both strands. Or more) chemically modified internucleotide linkages having Formula I. In another non-limiting example, exemplary siNA molecules of the invention have one or more chemically modified internucleotide linkages having Formula I on the sense strand, antisense strand, or both strands ( For example, about 1,2,3,4,5,6,7,8,9,10 or more) pyrimidine nucleotides can be included. In yet another non-limiting example, an exemplary siNA molecule of the invention has one or more chemically modified internucleotide linkages having Formula I on the sense strand, antisense strand, or both strands. More (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) purine nucleotides can be included. In another embodiment, siNA molecules of the invention having internucleotide linkages of Formula I also include chemically modified nucleotides or non-nucleotides having any of Formulas I-VII.

［式中，
各Ｒ３，Ｒ４，Ｒ５，Ｒ６，Ｒ７，Ｒ８，Ｒ１０，Ｒ１１およびＲ１２は，独立して，Ｈ，ＯＨ，アルキル，置換アルキル，アルカリールまたはアラルキル，Ｆ，Ｃｌ，Ｂｒ，ＣＮ，ＣＦ３，ＯＣＦ３，ＯＣＮ，Ｏ−アルキル，Ｓ−アルキル，Ｎ−アルキル，Ｏ−アルケニル，Ｓ−アルケニル，Ｎ−アルケニル，ＳＯ−アルキル，アルキル−ＯＳＨ，アルキル−ＯＨ，Ｏ−アルキル−ＯＨ，Ｏ−アルキル−ＳＨ，Ｓ−アルキル−ＯＨ，Ｓ−アルキル−ＳＨ，アルキル−Ｓ−アルキル，アルキル−Ｏ−アルキル，ＯＮＯ２，ＮＯ２，Ｎ３，ＮＨ２，アミノアルキル，アミノ酸，アミノアシル，ＯＮＨ２，Ｏ−アミノアルキル，Ｏ−アミノ酸，Ｏ−アミノアシル，ヘテロシクロアルキル，ヘテロシクロアルカリール，アミノアルキルアミノ，ポリアルキルアミノ，置換シリル，または式１を有する基であり；Ｒ９は，Ｏ，Ｓ，ＣＨ２，Ｓ＝Ｏ，ＣＨＦ，またはＣＦ２であり，Ｂは，ヌクレオシド塩基，例えば，アデニン，グアニン，ウラシル，シトシン，チミン，２−アミノアデノシン，５−メチルシトシン，２，６−ジアミノプリン，または標的ＲＮＡに相補的であっても相補的でなくてもよい他の任意の天然に生じない塩基，または非ヌクレオシド塩基，例えば，フェニル，ナフチル，３−ニトロピロール，５−ニトロインドール，ネブラリン，ピリドン，ピリジノン，または標的ＲＮＡに相補的であっても相補的でなくてもよい他の任意の天然に生じない万能塩基である］
を有する１またはそれ以上（例えば，約１，２，３，４，５，６，７，８，９，１０個またはそれ以上）のヌクレオチドまたは非ヌクレオチドを含む。 In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, the chemical modification is of formula II:

[Where,
Each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, amino acid, aminoacyl, ONH2, O-aminoalkyl, O-amino acid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, poly Rylamino, substituted silyl, or a group having Formula 1; R9 is O, S, CH2, S = O, CHF, or CF2, and B is a nucleoside base, such as adenine, guanine, uracil, cytosine, Thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that may or may not be complementary to the target RNA, or non-nucleoside base , For example, phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebulaline, pyridone, pyridinone, or any other non-naturally occurring universal base that may or may not be complementary to the target RNA Is]
One or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) nucleotides or non-nucleotides.

  A chemically modified nucleotide or non-nucleotide of Formula II can be present in one or both oligonucleotide strands of the siNA duplex, eg, the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically modified nucleotides or non-nucleotides of Formula II, the 3 ′ end, 5 ′ end, or 3 ′ of the sense strand, antisense strand, or both strands. It can be included at both the end and the 5 'end. For example, exemplary siNA molecules of the invention can comprise from about 1 to about 5 or more (eg, about 1, 2, 3, 4, 5 or more) chemically modified nucleotides of formula II or Non-nucleotides can be included at the 5 ′ end of the sense strand, antisense strand, or both strands. In another non-limiting example, exemplary siNA molecules of the invention have about 1 to about 5 or more (eg, about 1, 2, 3, 4, 5 or more) chemistries of formula II. Modified nucleotides or non-nucleotides can be included at the 3 ′ end of the sense strand, the antisense strand, or both strands.

［式中，
各Ｒ３，Ｒ４，Ｒ５，Ｒ６，Ｒ７，Ｒ８，Ｒ１０，Ｒ１１およびＲ１２は，独立して，Ｈ，ＯＨ，アルキル，置換アルキル，アルカリールまたはアラルキル，Ｆ，Ｃｌ，Ｂｒ，ＣＮ，ＣＦ３，ＯＣＦ３，ＯＣＮ，Ｏ−アルキル，Ｓ−アルキル，Ｎ−アルキル，Ｏ−アルケニル，Ｓ−アルケニル，Ｎ−アルケニル，ＳＯ−アルキル，アルキル−ＯＳＨ，アルキル−ＯＨ，Ｏ−アルキル−ＯＨ，Ｏ−アルキル−ＳＨ，Ｓ−アルキル−ＯＨ，Ｓ−アルキル−ＳＨ，アルキル−Ｓ−アルキル，アルキル−Ｏ−アルキル，ＯＮＯ２，ＮＯ２，Ｎ３，ＮＨ２，アミノアルキル，アミノ酸，アミノアシル，ＯＮＨ２，Ｏ−アミノアルキル，Ｏ−アミノ酸，Ｏ−アミノアシル，ヘテロシクロアルキル，ヘテロシクロアルカリール，アミノアルキルアミノ，ポリアルキルアミノ，置換シリル，または式１を有する基であり；Ｒ９は，Ｏ，Ｓ，ＣＨ２，Ｓ＝Ｏ，ＣＨＦ，またはＣＦ２であり，Ｂは，ヌクレオシド塩基，例えば，アデニン，グアニン，ウラシル，シトシン，チミン，２−アミノアデノシン，５−メチルシトシン，２，６−ジアミノプリン，または標的ＲＮＡに相補的であっても相補的でなくてもよいように用いることができる他の任意の天然に生じない塩基，または非ヌクレオシド塩基，例えば，フェニル，ナフチル，３−ニトロピロール，５−ニトロインドール，ネブラリン，ピリドン，ピリジノン，または標的ＲＮＡに相補的であっても相補的でなくてもよい他の任意の天然に生じない万能塩基である］
を有する１またはそれ以上（例えば，約１，２，３，４，５，６，７，８，９，１０個またはそれ以上）のヌクレオチドまたは非ヌクレオチドを含む。 In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, the chemical modification is of formula III:

[Where,
Each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, amino acid, aminoacyl, ONH2, O-aminoalkyl, O-amino acid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, poly Rylamino, substituted silyl, or a group having Formula 1; R9 is O, S, CH2, S = O, CHF, or CF2, and B is a nucleoside base, such as adenine, guanine, uracil, cytosine, Thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other naturally occurring that can be used to be complementary or non-complementary to the target RNA Bases, or non-nucleoside bases such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebulaline, pyridone, pyridinone, or any other that may or may not be complementary to the target RNA It is a universal base that does not occur naturally]
One or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) nucleotides or non-nucleotides.

  A chemically modified nucleotide or non-nucleotide of formula III can be present in one or both oligonucleotide strands of the siNA duplex, eg, in the sense strand, antisense strand, or both strands. The siNA molecules of the present invention can contain one or more chemical compounds of Formula III at the 3 ′ end, 5 ′ end, or both 3 ′ and 5 ′ ends of the sense strand, antisense strand, or both strands. It can contain modified nucleotides or non-nucleotides. For example, exemplary siNA molecules of the invention have about 1 to about 5 or more (eg, about 1, 2, 3, 4, 5) at the 5 ′ end of the sense strand, antisense strand, or both strands. Or more) of formula III chemically modified nucleotides or non-nucleotides. In another non-limiting example, exemplary siNA molecules of the invention have about 1 to about 5 or more (eg, about 1, about 3) at the 3 ′ end of the sense strand, antisense strand, or both strands. 2, 3, 4, 5 or more) of chemically modified nucleotides or non-nucleotides of formula III.

  In another embodiment, the siNA molecule of the invention comprises a nucleotide having formula II or III, wherein the nucleotide having formula II or III is in an inverted configuration. For example, nucleotides having formula II or III can be siNA constructs in 3′-3 ′, 3′-2 ′, 2′-3 ′, or 5′-5 ′ configuration, eg, one or both of the siNA strands. Can be attached to the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end.

［式中，
各ＸおよびＹは，独立して，Ｏ，Ｓ，Ｎ，アルキル，置換アルキル，またはアルキルハロであり；各ＺおよびＷは，独立して，Ｏ，Ｓ，Ｎ，アルキル，置換アルキル，Ｏ−アルキル，Ｓ−アルキル，アルカリール，アラルキル，またはアルキルハロであり；Ｗ，Ｘ，ＹおよびＺはすべてＯではない］
を有する５’末端リン酸基を含む。 In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, the chemical modification is of formula IV:

[Where,
Each X and Y is independently O, S, N, alkyl, substituted alkyl, or alkylhalo; each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl , S-alkyl, alkaryl, aralkyl, or alkylhalo; W, X, Y, and Z are not all O]
5 'terminal phosphate group having

  In one embodiment, the invention features a siNA molecule having a 5 ′ terminal phosphate group with formula IV in a target-complementary strand, eg, a strand complementary to the target RNA, wherein the siNA molecule is , Including total RNA siNA molecules. In another aspect, the invention features a siNA molecule having a 5 ′ terminal phosphate group having formula IV in the target-complementary strand, wherein the siNA molecule is also 3 ′ of one or both strands. 3 'terminal nucleotide of about 1 to about 3 (eg, about 1, 2, or 3) nucleotides having about 1 to about 4 (eg, about 1, 2, 3, or 4) deoxyribonucleotides at the ends Includes overhangs. In another embodiment, the 5 ′ terminal phosphate group having formula IV is present in the target-complementary strand of a siNA molecule of the invention, eg, a siNA molecule having a chemical modification having any of formulas I-VII. .

  In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, the chemical modification includes one or more phosphorothioate internucleotide linkages. For example, in a non-limiting example, the present invention is chemically modified to have about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages on one siNA strand. Short interfering nucleic acids (siNA). In yet another embodiment, the present invention provides a chemically modified compound having independently about 1,2,3,4,5,6,7,8 or more phosphorothioate internucleotide linkages on both siNA strands. Characterized short interfering nucleic acids (siNA). The phosphorothioate internucleotide linkage can be present in one or both of the oligonucleotide strands of the siNA duplex, eg, in the sense strand, antisense strand, or both strands. The siNA molecule of the invention comprises one or more phosphorothioate internucleotide linkages at the 3 ′ end, 5 ′ end, or both 3 ′ and 5 ′ ends of the sense strand, antisense strand, or both strands. Can do. For example, exemplary siNA molecules of the invention have about 1 to about 5 or more (eg, about 1, 2, 3, 4, 5) at the 5 ′ end of the sense strand, antisense strand, or both strands. , Or more) consecutive phosphorothioate internucleotide linkages. In another non-limiting example, exemplary siNA molecules of the invention have one or more (eg, about 1, 2, 3, 4, 5, 6) on the sense strand, antisense strand, or both strands. , 7, 8, 9, 10 or more) pyrimidine phosphorothioate internucleotide linkages. In yet another non-limiting example, exemplary siNA molecules of the invention have one or more (eg, about 1, 2, 3, 4, 5, 5) on the sense strand, antisense strand, or both strands. 6,7,8,9,10 or more) purine phosphorothioate internucleotide linkages.

  In one embodiment, the invention provides a phosphorothioate internucleotide linkage having one or more sense strands, eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more sense strands, And / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) 2'-deoxy, 2'-O-methyl, 2 ' -Deoxy-2'-fluoro, and / or one or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base-modified nucleotides Optionally, including an end cap molecule at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the sense strand; and from about 1 to about 10 or more antisense strands, particularly about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 Or more phosphorothioate internucleotide linkages and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) 2'-deoxys , 2′-O-methyl, 2′-deoxy-2′-fluoro, and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or (Or more) universal base-modified nucleotides, optionally featuring a siNA molecule comprising an end cap molecule at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense strand. In another embodiment, one or more, eg, about 1,2,3,4,5,6,7,8,9,10 or more pyrimidine nucleotides of the sense and / or antisense siNA strands. Are chemically modified with 2'-deoxy, 2'-O-methyl and / or 2'-deoxy-2'-fluoro nucleotides and are present in the same or different strands, eg one or more, eg , About 1,2,3,4,5,6,7,8,9,10 or more phosphorothioate internucleotide linkages, and / or 3 'end, 5' end, or 3 'end and 5' end Both end cap molecules may or may not have end cap molecules.

  In another embodiment, the present invention relates to phosphorothioate internucleotide linkages of about 1 to about 5, especially about 1, 2, 3, 4, or 5 sense strands, and / or one or more (eg, about 1, 2, 3, 4, 5 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and / or one or more (eg, about 1, 2, 3, 4, 5 or more) universal base modified nucleotides, optionally including an end cap molecule at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the sense strand; And about 1 to about 5 or more antisense strands, particularly about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and / or one or more (eg, about 1, 2, 3, 4 5,6,7,8,9,10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more), optionally 3 ', 5', or 3 'end of the antisense strand And features siNA molecules containing end cap molecules at both the 5 'end. In another embodiment, one or more of the sense and / or antisense siNA strands, such as about 1,2,3,4,5,6,7,8,9,10 or more pyrimidine nucleotides, About 1 to about 5 or more chemically modified with 2'-deoxy, 2'-O-methyl and / or 2'-deoxy-2'-fluoro nucleotides, present in the same or different strands For example, having about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages and / or end cap molecules at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end. You may or may not have.

In one embodiment, the present invention provides a phosphorothioate internucleotide linkage having one or more antisense strands, eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. , And / or about 1 or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and / or one or more (eg, about 1, 2, 3, 4
, 5, 6, 7, 8, 9, 10, or more) universally modified nucleotides, optionally terminating at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the sense strand Between about 1 to about 10 or more, especially about 1,2,3,4,5,6,7,8,9,10 or more phosphorothioate nucleotides, including a cap molecule; Bonds, and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) universal base modified nucleotides And optionally the 3 ′ end, 5 ′ end, or 3 of the antisense strand Features siNA molecules that contain end-capping molecules at both the 'end and the 5' end. In another embodiment, one or more, eg, about 1,2,3,4,5,6,7,8,9,10 or more pyrimidine nucleotides of the sense and / or antisense siNA strands are , 2'-deoxy, 2'-O-methyl and / or 2'-deoxy-2'-fluoro nucleotides, one or more present in the same or different strands, eg about 1 , 2,3,4,5,6,7,8,9,10 or more phosphorothioate internucleotide linkages, and / or 3 ', 5', or both 3 'and 5' ends It may or may not have an end cap molecule.

  In another embodiment, the present invention provides about 1 to about 5 or more, especially about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages and / or 1 or More (eg, about 1,2,3,4,5,6,7,8,9,10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2 ' -Containing fluoro, and / or one or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, optionally the sense strand Including an end cap molecule at the 3 'end, 5' end, or both the 3 'end and the 5' end; and about 1 to about 5 or more antisense strands, particularly about 1, 2, 3, 4, 5 or more phosphorothioate nuts Inter-oxide bond, and / or one or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O- Methyl, 2′-deoxy-2′-fluoro, and / or one or more (eg, about 1,2,3,4,5,6,7,8,9,10 or more) universal bases Features siNA molecules that contain modified nucleotides and optionally end cap molecules at the 3 ′ end, 5 ′ end, or both 3 ′ and 5 ′ ends of the antisense strand. In another embodiment, one or more, eg, about 1,2,3,4,5,6,7,8,9,10 or more pyrimidine nucleotides of the sense and / or antisense siNA strands are , 2′-deoxy, 2′-O-methyl and / or 2′-deoxy-2′-fluoro nucleotides, and are present in about 1 to about 5 in the same or different strands, for example , Approximately 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages and / or end cap molecules at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end You may or may not have.

  In one embodiment, the present invention provides chemically modified compounds having about 1 to about 5, in particular about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages in each strand of the siNA molecule. Characterized short interfering nucleic acid (siNA) molecules.

In another aspect, the invention features a siNA molecule that includes a 2′-5 ′ internucleotide linkage. 2′-5 ′ internucleotide linkages can be present at one or both 3 ′ ends, 5 ′ ends, or both 3 ′ ends and 5 ′ ends of the siNA sequence strand. Furthermore, 2′-5 ′ internucleotide linkages can be present at various other positions in one or both of the siNA sequence strands, eg, about 1, 2 of pyrimidine nucleotides in one or both strands of the siNA molecule. , 3, 4, 5, 6, 7, 8, 9, 10 or more, eg, all internucleotide linkages can include 2′-5 ′ internucleotide linkages, or one or both of siNA molecules About 1,2,3,4,5,6,7,8,9,10 or more of the purine nucleotides of each strand, eg, all internucleotide linkages include 2′-5 ′ internucleotide linkages Can do.

  In another embodiment, a chemically modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically modified, each strand having from about 18 to about 27 (Eg, about 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27) nucleotides in length, and duplexes are about 18 to about 23 (eg, about 18, 19, 20, 21). , 22, or 23) have a base pair and the chemical modification comprises a structure having any of formulas I-VII. For example, exemplary chemically modified siNA molecules of the invention include duplexes with two chains, one or both of which are chemical modifications having any of the formulas I-VII or any combination thereof. It may be chemically modified, each strand consists of about 21 nucleotides, each with a 2-nucleotide 3 'terminal nucleotide overhang, and the duplex has about 19 base pairs. In another embodiment, the siNA molecule of the invention has a single stranded hairpin structure, wherein the siNA is about 36 to about 70 (eg, about 36, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length and having about 18 to about 23 (eg, about 18, 19, 20, 21, 22, or 23) base pairs, and siNA is any of formulas I-VII or any of them Chemical modifications including structures having a combination of For example, exemplary chemically modified siNA molecules of the present invention can be about 42 to about 50 (chemically modified with a chemical modification having any of the formulas I-VII or any combination thereof. For example, a linear oligonucleotide having about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides, wherein the linear oligonucleotide comprises about 19 base pairs and 2-nucleotides Form a hairpin structure with a 3 ′ terminal nucleotide overhang. In another embodiment, the linear hairpin siNA molecule of the invention comprises a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. For example, a linear hairpin siNA molecule of the present invention can be obtained when a double-stranded siNA molecule having a 3 ′ terminal overhang, such as a 3 ′ terminal nucleotide overhang comprising about 2 nucleotides, by in vivo degradation of the loop portion of the siNA molecule. Designed to be generated.

  In another embodiment, the siNA molecule of the invention comprises a circular nucleic acid molecule, wherein the siNA is from about 38 to about 70 (eg, about 38, 40, 45, 50, 55, 60, 65, or 70) nucleotides. And having about 18 to about 23 (eg, about 18, 19, 20, 21, 22, or 23) base pairs, siNA can include chemical modifications, which can be represented by the formula I- Includes structures having any of VII or any combination thereof. For example, exemplary chemically modified siNA molecules of the present invention can have from about 42 to about 50 (e.g., chemically modified with a chemical modification having any of Formulas I-VII or any combination thereof) , About 42, 43, 44, 45, 46, 47, 48, 49, or 50) a cyclic oligonucleotide having nucleotides, the circular oligonucleotide having a dumbbell-shaped structure having about 19 base pairs and two loops. Form.

  In another embodiment, the cyclic siNA molecule of the invention comprises two loop motifs, wherein one or both of the loop portions of the siNA molecule are biodegradable. For example, a cyclic siNA molecule of the invention can be generated by in vivo degradation of the loop portion of the siNA molecule to produce a double stranded siNA molecule having a 3 ′ terminal overhang, eg, a 3 ′ terminal nucleotide overhang comprising about 2 nucleotides. Designed to be able to.

［式中，
各Ｒ３，Ｒ４，Ｒ５，Ｒ６，Ｒ７，Ｒ８，Ｒ１０，Ｒ１１，Ｒ１２，およびＲ１３は，独立して，Ｈ，ＯＨ，アルキル，置換アルキル，アルカリールまたはアラルキル，Ｆ，Ｃｌ，Ｂｒ，ＣＮ，ＣＦ３，ＯＣＦ３，ＯＣＮ，Ｏ−アルキル，Ｓ−アルキル，Ｎ−アルキル，Ｏ−アルケニル，Ｓ−アルケニル，Ｎ−アルケニル，ＳＯ−アルキル，アルキル−ＯＳＨ，アルキル−ＯＨ，Ｏ−アルキル−ＯＨ，Ｏ−アルキル−ＳＨ，Ｓ−アルキル−ＯＨ，Ｓ−アルキル−ＳＨ，アルキル−Ｓ−アルキル，アルキル−Ｏ−アルキル，ＯＮＯ２，ＮＯ２，Ｎ３，ＮＨ２，アミノアルキル，アミノ酸，アミノアシル，ＯＮＨ２，Ｏ−アミノアルキル，Ｏ−アミノ酸，Ｏ−アミノアシル，ヘテロシクロアルキル，ヘテロシクロアルカリール，アミノアルキルアミノ，ポリアルキルアミノ，置換シリル，または式１を有する基であり；Ｒ９は，Ｏ，Ｓ，ＣＨ２，Ｓ＝Ｏ，ＣＨＦ，またはＣＦ２である］
を有する化合物を含む。 In one embodiment, the siNA molecule of the invention has at least one (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) abasic components, such as , Formula V:

[Where,
Each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3. , OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl -SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, amino acid, aminoacyl, ONH2, O-aminoalkyl, O -Amino acids, O-aminoacyls, heterocycloalkyls, heterocycloalkaryls, aminoalkyla Bruno, polyalkylamino, substituted silyl, or a group having the formula 1; R9 is, O, is S, CH2, S = O, CHF, or, CF2]
A compound having

［式中，
各Ｒ３，Ｒ４，Ｒ５，Ｒ６，Ｒ７，Ｒ８，Ｒ１０，Ｒ１１，Ｒ１２，およびＲ１３は，独立して，Ｈ，ＯＨ，アルキル，置換アルキル，アルカリールまたはアラルキル，Ｆ，Ｃｌ，Ｂｒ，ＣＮ，ＣＦ３，ＯＣＦ３，ＯＣＮ，Ｏ−アルキル，Ｓ−アルキル，Ｎ−アルキル，Ｏ−アルケニル，Ｓ−アルケニル，Ｎ−アルケニル，ＳＯ−アルキル，アルキル−ＯＳＨ，アルキル−ＯＨ，Ｏ−アルキル−ＯＨ，Ｏ−アルキル−ＳＨ，Ｓ−アルキル−ＯＨ，Ｓ−アルキル−ＳＨ，アルキル−Ｓ−アルキル，アルキル−Ｏ−アルキル，ＯＮＯ２，ＮＯ２，Ｎ３，ＮＨ２，アミノアルキル，アミノ酸，アミノアシル，ＯＮＨ２，Ｏ−アミノアルキル，Ｏ−アミノ酸，Ｏ−アミノアシル，ヘテロシクロアルキル，ヘテロシクロアルカリール，アミノアルキルアミノ，ポリアルキルアミノ，置換シリル，または式Ｉを有する基であり；Ｒ９は，０，Ｓ，ＣＨ２，Ｓ＝０，ＣＨＦ，またはＣＦ２であり，Ｒ２，Ｒ３，Ｒ８またはＲ１３のいずれかは，本発明のｓｉＮＡ分子への結合の点として働く］
を有する化合物を含む。 In one embodiment, the siNA molecule of the invention has at least one (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) inverted abasic components, For example, the formula VI:

[Where,
Each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3. , OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl-OH, O-alkyl -SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, amino acid, aminoacyl, ONH2, O-aminoalkyl, O -Amino acids, O-aminoacyls, heterocycloalkyls, heterocycloalkaryls, aminoalkyla R9 is 0, S, CH2, S = 0, CHF, or CF2, and any of R2, R3, R8, or R13 is: Acts as a point of attachment to the siNA molecule of the present invention]
A compound having

［式中，各ｎは，独立して，１−１２の整数であり，各Ｒ１，Ｒ２およびＲ３は，独立して，Ｈ，ＯＨ，アルキル，置換アルキル，アルカリールまたはアラルキル，Ｆ，Ｃｌ，Ｂｒ，ＣＮ，ＣＦ３，ＯＣＦ３，ＯＣＮ，Ｏ−アルキル，Ｓ−アルキル，Ｎ−アルキル，Ｏ−アルケニル，Ｓ−アルケニル，Ｎ−アルケニル，ＳＯ−アルキル，アルキル−ＯＳＨ，アルキル−ＯＨ，Ｏ−アルキル−ＯＨ，Ｏ−アルキル−ＳＨ，Ｓ−アルキル−ＯＨ，Ｓ−アルキル−ＳＨ，アルキル−Ｓ−アルキル，アルキル−Ｏ−アルキル，ＯＮＯ２，ＮＯ２，Ｎ３，ＮＨ２，アミノアルキル，アミノ酸，アミノアシル，ＯＮＨ２，Ｏ−アミノアルキル，Ｏ−アミノ酸，Ｏ−アミノアシル，ヘテロシクロアルキル，ヘテロシクロアルカリール，アミノアルキルアミノ，ポリアルキルアミノ，置換シリル，または式Ｉを有する基であり，Ｒ１，Ｒ２またはＲ３は，本発明のｓｉＮＡ分子への結合の点として働く］
を有する化合物を含む。 In another embodiment, the siNA molecule of the present invention has at least one (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) substituted polyalkyl moieties. , For example, Formula VII:

[Wherein each n is independently an integer of 1-12 and each R1, R2 and R3 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OSH, alkyl-OH, O-alkyl- OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-S-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, amino acid, aminoacyl, ONH2, O -Aminoalkyl, O-amino acid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino Polyalkylamino, a group having a substituted silyl or Formula I,, R1, R2 or R3 serves as points of attachment to the siNA molecule of the invention]
A compound having

  In another embodiment, the invention provides that R1 and R2 are hydroxyl (OH) groups, n is 1, R3 contains O, and one or both strands of the double stranded siNA molecule of the invention. Features a compound having the formula VII that is the point of binding to the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end, or to the single-stranded siNA molecule of the invention. This modification is referred to herein as “glyceryl” (see, for example, modification 6 in FIG. 10).

  In another embodiment, a component of the invention having either formula V, VI or VII is present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the siNA molecule of the invention. . For example, the component having the formula V, VI or VII can be at the 3 ′ end, 5 ′ end, or 3 ′ end and 5 ′ end of the antisense strand, sense strand, or both antisense strand and sense strand of the siNA molecule. Can exist in both. In addition, the component having Formula VII can be present at the 3 'end or 5' end of the hairpin siNA molecule, as described herein.

  In another embodiment, the siNA molecule of the invention comprises an abasic residue having the formula V or VI, wherein the abasic residue having the formula VI or VI is 3′-3 ′, 3′- In 2 ′, 2′-3 ′, or 5′-5 ′ configurations, for example, siNA constructs at the 3 ′ end, 5 ′ end, or both 3 ′ and 5 ′ ends of one or both siNA strands Are connected.

  In one embodiment, the siNA molecule of the invention has one or more (eg, at the 5 ′ end, 3 ′ end, both 5 ′ end and 3 ′ end, or any combination thereof, eg, siNA molecule). , About 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) lock nucleic acid (LNA) nucleotides.

In another embodiment, the siNA molecule of the invention comprises, for example, 1 at the 5 ′ end, 3 ′ end, both 5 ′ end and 3 ′ end of the siNA molecule, or any combination thereof.
Or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) acyclic nucleotides.

  In one embodiment, the invention features a chemically modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically modified siNA comprises a sense region, wherein Any (eg, one or more, or all) pyrimidine nucleotides present are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidines). Any (eg, one or more, or all) purine nucleotides that are nucleotides, or where multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), and are present in the sense region Is a 2'-deoxypurine nucleotide (eg all pre Or nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides).

  In one embodiment, the invention features a chemically modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically modified siNA comprises a sense region, wherein Any (eg, one or more, or all) pyrimidine nucleotides present are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides). Or any pyrimidine nucleotides are -deoxy-2'-fluoropyrimidine nucleotides) and any (eg, one or more or all) purine nucleotides present in the sense region are 2 ' -Deoxypurine nucleotides (eg all purine nucleosides) The nucleotide is a 2′-deoxypurine nucleotide, or the plurality of purine nucleotides is a 2′-deoxypurine nucleotide), wherein any nucleotide containing a 3 ′ terminal nucleotide overhang present in the sense region is 2'-deoxynucleotide.

  In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically modified siNA comprises an antisense region, wherein the antisense region Any (eg, one or more, or all) pyrimidine nucleotides present in it are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Fluoropyrimidine nucleotides or multiple pyrimidine nucleotides are 2'-deoxy-2'-fluoropyrimidine nucleotides) and any (eg, one or more, or all) present in the antisense region ) Purine nucleotides are 2'-O-methylpurine nucleotides ( Example, wherein all purine nucleotides are 2'-O- methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O- methyl purine nucleotides).

In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically modified siNA comprises an antisense region, wherein the antisense region Any (eg, one or more, or all) pyrimidine nucleotides present in it are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Fluoropyrimidine nucleotides or multiple pyrimidine nucleotides are 2'-deoxy-2'-fluoropyrimidine nucleotides) and any (eg, one or more, or all) present in the antisense region ) Purine nucleotides are 2′-O-methylpurine nucleotides (eg, All purine nucleotides are 2'-O-methylpurine nucleotides or multiple purine nucleotides are 2'-O-methylpurine nucleotides), where the 3 'end is present in the antisense region Any nucleotide containing a nucleotide overhang is a 2'-deoxy nucleotide.

  In one aspect, the invention features a chemically modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically modified siNA comprises an antisense region, wherein Any (eg, one or more, or all) pyrimidine nucleotides present in are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′-fluoro Any (eg, one or more, or all) of pyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides) and present in the antisense region Purine nucleotides are 2'-deoxypurine nucleotides (eg, , Wherein all purine nucleotides are 2'-deoxy purine nucleotides, or a plurality of purine nucleotides are 2'-deoxy purine nucleotides).

  In one embodiment, the present invention provides a chemically modified short interfering nucleic acid (siNA) molecule of the present invention capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system. Wherein the chemically modified siNA comprises a sense region, wherein one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoropyrimidine nucleotides ( For example, all pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), which are present in the sense region 1 Or more purine nucleotides are 2'-deoxypurine nucleotides (For example, all purine nucleotides are 2′-deoxy purine nucleotides or multiple purine nucleotides are 2′-deoxy purine nucleotides), and the 3 ′ end, 5 ′ end of the sense region, Or an inverted deoxyabasic modification that may be present at both the 3 ′ end and the 5 ′ end, with about 1 to about 4 additional sense regions (eg, about 1, 2, 3, or 4) A 3 ′ terminal overhang with 2′-deoxyribonucleotides of the same; and the chemically modified short interfering nucleic acid molecule comprises an antisense region, wherein 1 present in the antisense region Or more pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides). The dinucleotide is a 2′-deoxy-2′-fluoropyrimidine nucleotide or the plurality of pyrimidine nucleotides is a 2′-deoxy-2′-fluoropyrimidine nucleotide), one or more present in the antisense region The purine nucleotides are 2'-O-methyl purine nucleotides (eg, all purine nucleotides are 2'-O-methyl purine nucleotides or multiple purine nucleotides are 2'-O-methyl purine nucleotides) ), And end cap modifications, eg, any of the modifications described herein or shown in FIG. 10, which optionally include the 3 ′ end, 5 ′ end, or 3 ′ of the antisense sequence. It may be present at both the end and the 5 'end and the antisense region is Further optionally, it may comprise a 3 ′ terminal nucleotide overhang having about 1 to about 4 (eg, about 1, 2, 3, or 4) 2′-deoxy nucleotides, wherein the overhang nucleotide Can further include one or more (eg, 1, 2, 3, or 4) phosphorothioate internucleotide linkages. Non-limiting examples of these chemically modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein.

In one embodiment, the present invention provides a chemically modified short interfering nucleic acid (siNA) molecule of the present invention capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system. Where siNA includes a sense region, where:
One or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides, Alternatively, multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides) and one or more purine nucleotides present in the sense region are purine ribonucleotides (eg, all purine nucleotides are purine ribonucleotides). Inversion that may be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the sense region, and the purine nucleotides are purine ribonucleotides). Contains deoxy-abasic modification and Optionally further comprising a 3 ′ terminal overhang having about 1 to about 4 (eg, about 1, 2, 3, or 4) 2′-deoxyribonucleotides; and siNA is an antisense region Wherein one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2 ′ A fluoropyrimidine nucleotide or a plurality of pyrimidine nucleotides is a 2′-deoxy-2′-fluoropyrimidine nucleotide), and any purine nucleotide present in the antisense region is a 2′-O-methylpurine nucleotide. Yes (for example, all purine nucleotides are 2'-O-methylpurine And a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and end-cap modifications, such as any of the modifications described herein or shown in FIG. This may optionally be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, optionally further comprising from about 1 to about 4 antisense regions (eg, about It may include a 3 ′ terminal nucleotide overhang having 1, 2, 3, or 4 2′-deoxy nucleotides, wherein the overhang nucleotide further comprises one or more (eg, 1, 2, 3 or 4) phosphorothioate internucleotide linkages. Non-limiting examples of these chemically modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein.

In one embodiment, the present invention provides a chemically modified short interfering nucleic acid (siNA) molecule of the present invention capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system. Characterized and chemically modified siNA includes a sense region, wherein one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (eg, all Of the pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), for example, 1 or Further purine nucleotides are 2'-deoxynucleotides, Selected from the group consisting of nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (eg, all purine nucleotides are 2′-deoxynucleotides, lock nucleic acids (LNA) selected from the group consisting of nucleotide, 2′-methoxyethyl nucleotide, 4′-thionucleotide, and 2′-O-methyl nucleotide, or a plurality of purine nucleotides are 2′-deoxynucleotides, lock nucleic acids (LNA) selected from the group consisting of nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides), and optionally the 3 ′ end, 5 ′ end of the sense region, Or inverted deoxy-abasic modifications at both the 3 'and 5' ends And the sense region optionally further comprises a 3 ′ terminal overhang having about 1 to about 4 (eg, about 1, 2, 3, or 4) 2′-deoxyribonucleotides. And the chemically modified short interfering nucleic acid molecule comprises an antisense region, wherein one or more pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoropyrimidines An antisense region that is a nucleotide (eg, all pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides) One or more purine nucleotides present therein are 2′-deoxynucleotides, Selected from the group consisting of nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (eg, all purine nucleotides are 2′-deoxynucleotides, lock nucleic acids ( LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides, or a plurality of purine nucleotides are 2′-deoxynucleotides, lock nucleic acids (LNA) ) Selected from the group consisting of nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides), and end-cap modifications, such as those described or illustrated herein Including any of the modifications shown in Optionally, it may be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, optionally further comprising about 1 to about 4 antisense regions (eg, about It may also contain a 3 ′ terminal nucleotide overhang with 1, 2, 3, or 4 2′-deoxynucleotides, where the overhanging nucleotide further comprises one or more (eg 1,2,3). , Or 4) phosphorothioate internucleotide linkages.

  In another embodiment, any modified nucleotide present in the siNA molecule of the invention is preferably present in the antisense strand of the siNA molecule of the invention, but also optionally with the sense and / or antisense strand. It may be present on both sense strands, including modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules comprising modified nucleotides having a Northern conformation (see, eg, Northern pseudo-rotation cycle, eg, Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). Thus, chemically modified nucleotides present in the siNA molecules of the invention are preferably present in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and / or antisense strand and It may be present on both sense strands, which is resistant to nuclease degradation while maintaining the ability to mediate RNAi. Non-limiting examples of nucleotides having a Northern configuration include: lock nucleic acid (LNA) nucleotides (eg, 2′-O, 4′-C-methylene- (D-ribofuranosyl) nucleotides); 2′-methoxyethoxy (MOE) ) Nucleotides; 2'-methyl-thio-ethyl, 2'-deoxy-2'-fluoro nucleotides, 2'-deoxy-2'-chloronucleotides, 2'-azido nucleotides, and 2'-O-methyl nucleotides It is done.

In one aspect, the invention features a chemically modified short interfering nucleic acid molecule (siNA) capable of mediating RNA interference (RNAi) against HCV within a cell or in a reconstituted in vitro system, Here, a chemical modification includes a conjugate covalently linked to a chemically modified siNA molecule. In another embodiment, the conjugate is covalently attached to the chemically modified siNA molecule via a biodegradable linker. In one embodiment, the conjugate molecule is attached to the 3 ′ end of the sense strand, antisense strand, or both strands of the chemically modified siNA molecule. In another embodiment, the conjugate molecule is attached to the 5 ′ end of the sense strand, antisense strand, or both strands of the chemically modified siNA molecule. In yet another embodiment, the conjugate molecule is on the sense strand, antisense strand, or both 3 ′ and 5 ′ ends of both strands of the chemically modified siNA molecule, or any combination thereof. Are connected. In one embodiment, a conjugate molecule of the invention includes a molecule that facilitates delivery of a chemically modified siNA molecule to a biological system (eg, a cell). In another embodiment, the conjugate molecule conjugated to a chemically modified siNA molecule is polyethylene glycol, human serum albumin, or a ligand for a cellular receptor capable of mediating cellular uptake. Examples of specific conjugate molecules contemplated by the present invention that can be conjugated to chemically modified siNA molecules are described in Vargeese et al. (US patent application Ser. No. 10 / 201,394, hereby incorporated by reference). To quote). The type of conjugate used and the degree of conjugation of the siNA molecules of the present invention, while at the same time maintaining the ability of siNA to mediate RNAi activity, improved pharmacokinetic profile of the siNA construct, bioavailability, and / or Alternatively, stability can be evaluated. Thus, one of skill in the art can screen siNA constructs modified with various conjugates, for example, in animal models commonly known in the art, to determine the ability of the siNA conjugate complex to mediate RNAi. It can be determined whether it has improved properties while maintaining.

In one embodiment, the invention provides a short interfering nucleic acid (siNA) of the invention wherein the siNA further comprises a nucleotide, non-nucleotide, or mixed nucleotide / non-nucleotide linker that links the sense region of the siNA and the antisense region of the siNA. Characterized by molecules. In one embodiment, the nucleotide linkers of the present invention can be linkers that are 2 or more nucleotides in length, eg, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In another embodiment, the nucleotide linker may be a nucleic acid aptamer. As used herein, “aptamer” or “nucleic acid aptamer” means a nucleic acid molecule that specifically binds to a target molecule, where the nucleic acid molecule is recognized by the target molecule in its natural setting. It has a sequence containing sequence. Alternatively, aptamers may be nucleic acid molecules that bind to target molecules that do not naturally bind to nucleic acids. The target molecule can be any molecule of interest. For example, aptamers can be used to bind to the ligand binding domain of a protein, thereby preventing naturally occurring interactions between the ligand and the protein. This is a non-limiting example, and those skilled in the art will recognize that other embodiments can be readily generated using techniques generally known in the art (eg, Gold et al., 1995, Annu). Rev. Biochem., 64, 763; Brody and Gold, 2000, J: Biotechnol., 74, 5; Sun, 2000, Curr. 74, 27; Hermann and Patel, 2000, Science, 287, 820; and Jayasena, 1999, Clinical.
Chemistry, 45, 1628).

In yet another embodiment, the non-nucleotide linkers of the present invention include abasic nucleotides, polyethers, polyamines, polyamides, peptides, carbohydrates, lipids, polyhydrocarbons, or other polymeric compounds (eg, polyethylene glycols such as 2-100 ethylene glycol units). Specific examples include Seela and Kaiser, Nucleic Acids Res. 1990, 75: 6353 and Nucleic Acids Res. 1987, 75: 3113; Cload
and Schepartz, J. et al. Am. Chem. Soc. 1991, 173: 6324; Richardson and Schepartz, J. Am. Am. Chem. Soc. 1991, 773: 5109; Ma et al. , Nucleic Acids Res. 1993, 27: 2585 and Biochemistry 1993, 32: 1751; Durand et al. , Nucleic Acids Res. 1990, 75: 6353; McCurdy et al. , Nucleosides & Nucleotides 1991, 10: 287; Jschke et al. Tetrahedron Lett. 1993, 34: 301; Ono et al. Biochemistry 1991, 30: 9914; Arnold et al. , International Publication WO 89/02439; Usman et al. , International Publication WO 95/06731; Dudycz et al. , International Publication WO 95/11910 and Ferentz and
Verdine, J .; Am. Chem. Soc. 1991, 773: 4000 (all cited herein as part of this specification). "Non-nucleotides" can also be incorporated into nucleic acid strands by either sugar and / or phosphate substitution instead of one or more nucleotide units, allowing the remaining bases to exert their enzymatic activity Is any group or compound. A group or compound may be abasic if it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine, for example at the C1 position of the sugar.

  In one aspect, the invention features a short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) within a cell or in a reconstituted in vitro system, wherein two separate oligonucleotides One or both strands of the siNA molecule assembled from do not contain ribonucleotides. For example, siNA molecules can be assembled from a single oligonucleotide, where the sense and antisense regions of the siNA are ribonucleotides present in the oligonucleotide (eg, nucleotides having a 2′-OH group). Including separate oligonucleotides that do not have In another example, siNA molecules can be assembled from a single oligonucleotide, wherein the siNA sense and antisense regions are linked by a nucleotide or non-nucleotide linker as described herein. It is cyclized and the oligonucleotide does not have any ribonucleotides present in the oligonucleotide (eg, nucleotides having a 2′-OH group). Applicants have surprisingly found that the presence of ribonucleotides (eg, nucleotides having a 2'-hydroxyl group) in the siNA molecule is not necessary or essential to support RNAi activity. Thus, in one embodiment, all positions in the siNA are chemically modified nucleotides and / or non-nucleotides, eg, formula I, to the extent that the siNA molecule retains the ability to support RNAi activity in the cell. , II, III, IV, V, VI, or VII can include nucleotides or non-nucleotides or any combination thereof.

  In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule is complementary to a target nucleic acid sequence. A single-stranded polynucleotide having In another embodiment, the single stranded siNA molecule of the invention comprises a 5 'terminal phosphate group. In another embodiment, the single-stranded siNA molecule of the invention comprises a 5 'terminal phosphate group and a 3' terminal phosphate group (eg, 2 ', 3'-cyclic phosphate). In another embodiment, the single stranded siNA molecule of the invention comprises from about 19 to about 29 nucleotides. In yet another embodiment, the single stranded siNA molecule of the invention comprises one or more chemically modified nucleotides or non-nucleotides described herein. For example, to the extent that the ability of the siNA molecule to support RNAi activity is maintained in the cell, all positions in the siNA molecule are chemically modified nucleotides, such as nucleotides having any of formulas I-VII or Any combination thereof can be included.

In one embodiment, the siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule has complementarity to a target nucleic acid sequence. One or more pyrimidine nucleotides comprising a single-stranded polynucleotide and present in the siNA are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), any purine nucleotide present in the antisense region is a 2′-O-methylpurine nucleotide (For example, all pudding nucleotis Is a 2′-O-methylpurine nucleotide, or multiple purine nucleotides are 2′-O-methylpurine nucleotides), and end-cap modifications, such as those described herein or in FIG. Which may optionally be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, and siNA may optionally further There may be from about 1 to about 4 (eg, about 1, 2, 3, or 4) terminal 2′-deoxy nucleotides at the 3 ′ end, wherein the terminal nucleotide further comprises one or more ( (E.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and the siNA can optionally further comprise a terminal phosphate group, such as a 5 'terminal phosphate group. That.

  In one embodiment, the siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule has complementarity to a target nucleic acid sequence. One or more pyrimidine nucleotides comprising a single-stranded polynucleotide and present in the siNA are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), and any purine nucleotide present in the antisense region is a 2′-deoxypurine nucleotide ( For example, all processes Nucleotides are 2′-deoxypurine nucleotides or multiple purine nucleotides are 2′-deoxypurine nucleotides), and end-cap modifications, such as any described herein or shown in FIG. Which may optionally be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, and siNA further optionally at the 3 ′ end of the siNA molecule. About 1 to about 4 (eg, about 1, 2, 3, or 4) terminal 2′-deoxy nucleotides may be included, wherein the terminal nucleotide is further one or more (eg, 1, 2, , 3, or 4) phosphorothioate internucleotide linkages, and the siNA optionally further comprises a terminal phosphate group, eg, a 5 ′ terminal ligand. It can contain an acid group.

  In one embodiment, the siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule has complementarity to a target nucleic acid sequence. One or more pyrimidine nucleotides comprising a single-stranded polynucleotide and present in the siNA are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Any purine nucleotides present in the antisense region are lock nucleic acid (LNA) nucleotides (e.g., fluoropyrimidine nucleotides or multiple pyrimidine nucleotides are 2'-deoxy-2'-fluoropyrimidine nucleotides) (e.g. , All pudding Including, but is not limited to, any of the modifications described herein or shown in FIG. 10, and end cap modifications. May be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, and optionally, siNA may be present at about 1 to about 4 at the 3 ′ end of the siNA molecule. (Eg, about 1, 2, 3, or 4) terminal 2′-deoxynucleotides, wherein the terminal nucleotide is further one or more (eg, 1, 2, 3, or 4). ), And the siNA can optionally further comprise a terminal phosphate group, such as a 5 ′ terminal phosphate group.

In one embodiment, the siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule has complementarity to a target nucleic acid sequence. One or more pyrimidine nucleotides comprising a single-stranded polynucleotide and present in the siNA are 2′-deoxy-2′-fluoropyrimidine nucleotides (eg, all pyrimidine nucleotides are 2′-deoxy-2′- Fluoropyrimidine nucleotides, or multiple pyrimidine nucleotides are 2′-deoxy-2′-fluoropyrimidine nucleotides), and any purine nucleotide present in the antisense region is a 2′-methoxyethyl purine nucleotide (For example, all puddings Nucleotides are 2′-methoxyethylpurine nucleotides, or multiple purine nucleotides are 2′-methoxyethylpurine nucleotides), and end-cap modifications, such as those described herein or shown in FIG. Which may optionally be present at the 3 ′ end, 5 ′ end, or both the 3 ′ end and the 5 ′ end of the antisense sequence, and siNA may optionally further be present in the siNA molecule. There may be from about 1 to about 4 (eg, about 1, 2, 3, or 4) terminal 2′-deoxy nucleotides at the 3 ′ end, where the terminal nucleotide further comprises one or more (eg, , 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and siNA may optionally further include a terminal phosphate group, eg, a 5 ′ end. It is possible to include a phosphate group.

In another embodiment, any modified nucleotide present in a single stranded siNA molecule of the invention comprises a modified nucleotide having properties or characteristics similar to a naturally occurring ribonucleotide. For example, the present invention provides for a Northern conformation (eg, Northern pseudocycle (eg, Saenger, Principles).
of Nucleic Acid Structure, Springer-Verlag ed. , 1984)), and features siNA molecules comprising modified nucleotides. Thus, chemically modified nucleotides present in single stranded siNA molecules of the present invention are preferably resistant to nuclease degradation while maintaining the ability to mediate RNAi.

  In one aspect, the invention features a method of modulating HCV gene expression in a cell comprising: (a) synthesizing a siNA molecule of the invention, which may be chemically modified. Well, one of the siNA strands contains a sequence complementary to the RNA of the HCV gene; and (b) introduces the siNA molecule into the cell under conditions suitable to regulate the expression of the HCV gene in the cell. .

  In one aspect, the invention features a method of modulating HCV gene expression in a cell comprising: (a) synthesizing a siNA molecule of the invention, which may be chemically modified. Well, one of the siNA strands contains a sequence complementary to the RNA of the HCV gene, the sense strand sequence of the siNA contains the same sequence as that of the target RNA; and (b) regulates the expression of the HCV gene in the cell Introducing the siNA molecule into the cell under conditions suitable for.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in a cell, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene; and (b) introducing the siNA molecule into the cell under conditions suitable to regulate the expression of the HCV gene in the cell, Including that.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in a cell, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene, the sense strand sequence of the siNA comprises a sequence identical to the sequence of the target RNA; and (b) expression of the HCV gene in the cell Introducing the siNA molecule into the cell under conditions suitable to regulate.

  In one aspect, the invention features a method of modulating HCV gene expression in a tissue explant, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. One of the siNA strands may comprise a sequence complementary to the RNA of the HCV gene; and (b) identifying the siNA molecule under conditions suitable to regulate expression of the HCV gene in tissue explant Including introduction into cells of tissue explants derived from living organisms. In another embodiment, the method further returns the tissue explant to the organism from which the tissue is derived or introduced into another organism under conditions suitable to modulate the expression of the HCV gene in the organism. Including that.

  In one aspect, the invention features a method of modulating HCV gene expression in a tissue explant, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene, the sense strand sequence of the siNA comprises a sequence identical to the sequence of the target RNA; and (b) the HCV gene in the tissue explant. Introducing siNA molecules into cells of tissue explants derived from a particular organism under conditions suitable to regulate expression. In another embodiment, the method further returns the tissue explant to the organism from which the tissue is derived or introduced into another organism under conditions suitable to modulate the expression of the HCV gene in the organism. Including that.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in a tissue explant, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene; and (b) a siNA molecule under conditions suitable to regulate the expression of the HCV gene in tissue explants. To the cells of tissue explants derived from specific organisms. In another embodiment, the method further returns the tissue explant to the organism from which the tissue is derived or introduced into another organism under conditions suitable to modulate the expression of the HCV gene in the organism. Including that.

  In one aspect, the invention features a method of modulating HCV gene expression in an organism, the method comprising (a) synthesizing a siNA molecule of the invention, which may be chemically modified. , One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene; and (b) introducing the siNA molecule into the organism under conditions suitable to regulate the expression of the HCV gene in the organism.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in an organism, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. One of the siNA strands comprises a sequence complementary to the RNA of the HCV gene; and (b) introducing the siNA molecule into the organism under conditions suitable to regulate the expression of the HCV gene in the organism. including.

  In one aspect, the invention features a method of modulating HCV gene expression in a cell comprising: (a) synthesizing a siNA molecule of the invention, which may be chemically modified. Well, siNA comprises a single stranded sequence having complementarity to the RNA of the HCV gene; and (b) introducing the siNA molecule into the cell under conditions suitable to regulate the expression of the HCV gene in the cell. Including.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in a cell comprising: (a) synthesizing a siNA molecule of the invention, which is chemically modified. The siNA may comprise a single stranded sequence having complementarity to the RNA of the HCV gene; and (b) the siNA molecule may be in vitro or in vivo under conditions suitable to regulate the expression of the HCV gene in the cell. In contact with cells.

  In one aspect, the invention features a method of modulating HCV gene expression in a tissue explant, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. The siNA comprises a single stranded sequence complementary to the RNA of the HCV gene; and (b) identifies the siNA molecule under conditions suitable to regulate the expression of the HCV gene in tissue explants. In contact with cells of tissue explants derived from other organisms. In another embodiment, the method further returns the tissue explant to the organism from which the tissue is derived or introduced into another organism under conditions suitable to modulate the expression of the HCV gene in the organism. Including that.

  In another aspect, the invention features a method of modulating expression of two or more HCV genes in a tissue explant, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically The siNA comprises a single stranded sequence complementary to the RNA of the HCV gene; and (b) siNA under conditions suitable to regulate the expression of the HCV gene in tissue explants. Introducing molecules into cells of tissue explants derived from specific organisms. In another embodiment, the method further returns the tissue explant to the organism from which the tissue is derived or introduced into another organism under conditions suitable to modulate the expression of the HCV gene in the organism. Including that.

  In one aspect, the invention features a method of modulating HCV gene expression in an organism, the method comprising (a) synthesizing a siNA molecule of the invention, which may be chemically modified. , SiNA comprises a single stranded sequence having complementarity to the RNA of the HCV gene; and (b) introducing the siNA molecule into the organism under conditions suitable to regulate the expression of the HCV gene in the organism. .

  In another aspect, the invention features a method of modulating the expression of two or more HCV genes in an organism, the method comprising (a) synthesizing a siNA molecule of the invention, which is chemically modified. The siNA comprises a single stranded sequence having complementarity to the RNA of the HCV gene; and (b) introducing the siNA molecule into the organism under conditions suitable to regulate the expression of the HCV gene in the organism. Including that.

  In one aspect, the invention features a method of modulating the expression of an HCV gene in an organism, the method comprising: contacting with the siNA molecule.

  In another aspect, the invention features a method of modulating the expression of two or more HCV genes in an organism, the method comprising: Contacting with one or more siNA molecules of the invention.

The siNA molecule of the present invention can be designed such that expression of a target (HCV) gene is inhibited by RNAi targeting various RNA molecules. In one embodiment, the siNA molecules of the invention are used to target various RNAs corresponding to the target gene. Non-limiting examples of such RNAs include messenger RNA (mRNA), alternative RNA splicing variants of the target gene, post-transcriptionally modified RNA of the target gene, target gene pre-mRNA, and / or RNA template . If alternative splicing results in a family of transcripts that are distinguished by the use of appropriate exons, the present invention specifically inhibits the function of gene family members by inhibiting gene expression with the appropriate exons. Or can be used to distinguish between them. For example, proteins containing alternatively spliced transmembrane domains can be expressed in both membrane-bound and secreted forms. By targeting an exon containing a transmembrane domain using the present invention, the functional importance of membrane-bound pharmaceutical targeting can be determined for secreted proteins. Non-limiting examples of uses of the invention associated with targeting these RNA molecules include therapeutic pharmaceutical uses, pharmaceutical discovery uses, molecular diagnostics and gene functional uses, and gene mapping, eg, siNAs of the invention Mapping of single nucleotide polymorphisms using molecules is included. Such applications can be performed using known gene sequences or from partial sequences available from expressed sequence tags (ESTs).

  In another embodiment, siNA molecules of the invention are used to target conserved sequences corresponding to gene families, eg, HCV family genes. As such, siNA molecules that target many HCV targets can provide increased therapeutic effects. In addition, siNA can be used to characterize gene function pathways in a variety of applications. For example, the present invention can be used to inhibit the activity of a target gene in a pathway and determine the function of an uncharacterized gene in gene function analysis, mRNA function analysis, or translation analysis. The present invention can be used to determine target gene pathways that may be involved in various diseases and health conditions for drug development. To understand gene expression pathways involved in the progression and / or maintenance of, for example, HCV infection, liver failure, hepatocellular carcinoma, cirrhosis and other indications that may be responsive to levels of HCV in cells or tissues Can be used.

  In one embodiment, the siNA molecule and / or method of the invention comprises a gene that encodes an RNA represented by a Genbank accession number, eg, a Genbank accession number (eg, a Genbank accession number shown in Table I) herein. Is used to inhibit the expression of the HCV gene encoding the RNA sequence represented by

  In one embodiment, the present invention provides: (a) generating a library of siNA constructs having a predetermined complexity, and (b) conditions suitable for determining an RNAi target site in a target RNA sequence. Wherein the method comprises assaying the siNA construct of (a) above. In another embodiment, the siNA molecule of (a) comprises a strand of fixed length, eg, about 23 nucleotides in length. In yet another embodiment, the siNA molecule of (a) is of different length, eg, about 19 to about 25 (eg, about 19, 20, 21, 22, 23, 24, or 25) nucleotides. Having a length of chain. In one embodiment, the assay can include a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can include a cell culture system in which the target RNA is expressed. In another embodiment, the target RNA fragment is analyzed for a level of cleavage detectable by, for example, gel electrophoresis, Northern blot analysis, or RNAse protection assay to determine the most appropriate target site in the target RNA sequence. . The target RNA sequence can be obtained as is known in the art, for example, by cloning and / or transcription for in vitro systems and cellular expression in in vivo systems.

In one aspect, the present invention provides (a) a predetermined complexity, eg 4 ^N (N is
indicates the number of nucleotides base paired in each of the strands of the siNA construct, eg, has a complexity of 4 ¹⁹ for a siNA construct with a 21 nucleotide sense and antisense strand with 19 base pairs) Each of generating a library of randomized siNA constructs; and (b) assaying the siNA construct of (a) above under conditions suitable for determining RNAi target sites in the target HCV RNA sequence A method comprising the steps. In another embodiment, the siNA molecule of (a) comprises a strand of fixed length, eg, about 23 nucleotides in length. In yet another embodiment, the siNA molecule of (a) is of different length, eg, about 19 to about 25 (eg, about 19, 20, 21, 22, 23, 24, or 25) nucleotides. Has a chain of length. In one embodiment, the assay can include a reconstituted in vitro siNA assay, as described in Example 6 herein. In another embodiment, the assay can include a cell culture system in which the target RNA is expressed. In another embodiment, fragments of HCV RNA are analyzed for levels of cleavage detectable by, for example, gel electrophoresis, Northern blot analysis, or RNAse protection assay to determine the most appropriate target site in the target HCV RNA sequence. To do. Target HCV RNA sequences can be obtained as is known in the art, for example, by cloning and / or transcription for in vitro systems, or by cellular expression in in vivo systems.

  In another embodiment, the invention comprises: (a) analyzing the sequence of an RNA target encoded by the target gene; (b) having a sequence complementary to one or more regions of the RNA of (a) Synthesizing a set of one or more siNA molecules; and (c) assaying the siNA molecules of (b) under conditions suitable for determining an RNAi target in the target RNA sequence. It is characterized by. In one embodiment, the siNA molecule of (b) has a fixed length, eg, a strand of about 23 nucleotides in length. In another embodiment, the siNA molecule of (b) is a chain of different length, eg, about 19 to about 25 (eg, about 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. Have In one embodiment, the assay may comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can include a cell culture system in which the target RNA is expressed. Fragments of the target RNA are analyzed for detectable levels of cleavage, eg, by gel electrophoresis, Northern blot analysis, or RNAse protection assay to determine the most appropriate target site in the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and / or transcription for in vitro systems and by expression in in vivo systems.

  By “target site” is meant a sequence in the target RNA that is “targeted” for cleavage mediated by siNA constructs that contain sequences complementary to the target sequence in the antisense region.

  “Detectable level of cleavage” means cleavage of the target RNA (and formation of the cleavage product RNA) sufficient to distinguish the cleavage product from the RNA background generated from random degradation of the target RNA. . For most detection methods, a cleavage product generated from 1-5% of the target RNA is sufficient to detect from the background.

  In one aspect, the invention features a composition comprising a siNA molecule of the invention, which may be chemically modified, in a pharmaceutically acceptable carrier or diluent. In another embodiment, the present invention provides a pharmaceutical composition comprising a siNA molecule of the present invention that targets one or more genes and may be chemically modified in a pharmaceutically acceptable carrier or diluent. Characterized by things. In another aspect, the invention features a method of treating or preventing a disease or condition in a subject, the method comprising subjecting the subject to a condition under conditions suitable for treatment or prevention of the disease or condition in the subject. Administration of the composition of the invention alone or in combination with one or more other therapeutic compounds. In yet another aspect, the invention features a method of reducing or preventing tissue rejection in a subject, the method comprising subjecting the subject to a composition of the invention under conditions suitable for reducing or preventing tissue rejection in the subject. Administration.

In another aspect, the invention features a method of evaluating an HCV gene target, the method comprising: (a) synthesizing a siNA molecule of the invention, which may be chemically modified and the siNA chain One of the sequences comprises a sequence complementary to the RNA of the HCV target gene; (b) the siNA molecule is converted into a cell, tissue, or cell under conditions suitable to regulate expression of the HCV target gene in a cell, tissue, or organism. Introducing into an organism; and (c) determining the function of the gene by assaying phenotypic changes in the cell, tissue, or organism.

  In another aspect, the invention features a method of assessing an HCV target, the method comprising (a) synthesizing a siNA molecule of the invention, which may be chemically modified and the siNA chain One of them comprises a sequence complementary to the RNA of the HCV target gene; (b) introducing the siNA molecule into the biological system under conditions suitable to regulate the expression of the HCV target gene in the biological system. And (c) determining the function of the gene by assaying for phenotypic changes in the biological system.

  “Biological system” means a material in a purified or unpurified form from a biological source such as, but not limited to, humans, animals, plants, insects, bacteria, viruses or other sources. , Where the system contains components necessary for RNAi activity. The term “biological system” includes, for example, cells, tissues, or organisms, or extracts thereof. The term biological system also includes a reconstituted RNAi system that can be used in an in vitro setting.

  By “phenotypic change” is meant any detectable cellular change that occurs in response to contact or treatment with a nucleic acid molecule of the invention (eg, siNA). Such detectable changes include, but are not limited to, shape, size, proliferation, motility, protein expression or RNA expression, or other physical or chemical that can be assayed by methods known in the art. Changes are included. Detectable changes also include reporter genes / molecules such as green fluorescent protein (GFP), or various tags used to identify the expressed protein, or any other cellular component that can be assayed. Expression is included.

  In one aspect, the invention features a kit containing a siNA molecule of the invention, which may be chemically modified to regulate expression of an HCV target gene in a cell, tissue, or organism. Can be used. In another aspect, the invention features a kit containing two or more siNA molecules of the invention, which may be chemically modified, which comprises two or more HCV target genes in a cell, tissue, or organism. Can be used to regulate the expression of.

  In one aspect, the invention features a cell containing one or more siNA molecules of the invention that may be chemically modified. In another embodiment, the cell containing the siNA molecule of the invention is a mammalian cell. In yet another embodiment, the cell containing the siNA molecule of the invention is a human cell.

  In one embodiment, synthesis of a siNA molecule of the invention, which may be chemically modified, comprises (a) synthesizing two complementary strands of the siNA molecule; (b) obtaining a double-stranded siNA molecule Annealing the two complementary strands together under conditions suitable for. In another embodiment, the synthesis of the two complementary strands of the siNA molecule is performed by solid phase oligonucleotide synthesis. In yet another embodiment, the synthesis of the two complementary strands of the siNA molecule is performed by solid phase tandem oligonucleotide synthesis.

In one aspect, the invention features a method of synthesizing a siNA duplex molecule, the method comprising: (a) synthesizing a first oligonucleotide sequence strand of the siNA molecule, wherein the first oligonucleotide The sequence strand includes a cleavable linker molecule that can be used as a scaffold for synthesis of the second oligonucleotide sequence strand of siNA; (b) a second oligonucleotide of siNA on the scaffold of the first oligonucleotide sequence strand A sequence strand is synthesized, wherein the second oligonucleotide sequence strand further comprises a chemical moiety that can be used to purify the siNA duplex; (c) the two siNA oligonucleotide strands are hybridized and stable Cleaving the linker molecule of (a) under conditions suitable to form a complex duplex; and d) utilizing the chemical moiety of the second oligonucleotide sequence strand purifying siNA duplex, comprising the steps of. In one embodiment, the cleavage of the linker molecule in (c) above is performed under hydrolysis conditions using, for example, an alkylamine base such as methylamine during deprotection of the oligonucleotide. In one embodiment, the method of synthesis includes solid phase synthesis on a solid support such as calibrated porous glass (CPG) or polystyrene, wherein the first sequence of (a) comprises solid support. Used as a scaffold and synthesized on a cleavable linker such as a succinyl linker. The cleavable linker used as a scaffold for synthesizing the second chain in (a) is a solid support so that the solid support derivatized linker and the cleavable linker of (a) are cleaved simultaneously. It can have the same reactivity as the derivatized linker. In another embodiment, the chemical moiety of (b) that can be used to isolate the bound oligonucleotide sequence comprises a trityl group, such as a dimethoxytrityl group, which in the tritylone synthesis strategy described herein. Can be used. In yet another embodiment, chemical components such as dimethoxytrityl groups are removed during purification using, for example, acidic conditions.

  In yet another embodiment, the method of siNA synthesis is solution phase synthesis or hybrid phase synthesis, wherein a cleavable linker attached to the first sequence and acting as a scaffold for the synthesis of the second sequence is used. Synthesize both strands of the siNA duplex in tandem. Double-stranded siNA molecules are formed by cleaving the linker under conditions suitable for the hybridization of separate siNA sequence strands.

  In another aspect, the invention features a method of synthesizing a siNA duplex molecule, the method comprising: (a) synthesizing one oligonucleotide sequence strand of a siNA molecule, wherein the sequence is the other oligonucleotide Comprising a cleavable linker molecule that can be used as a scaffold for synthesis of the sequence; (b) synthesizing a second oligonucleotide sequence having complementarity to the first sequence strand on the scaffold of (a); Wherein the second sequence comprises the other strand of the double stranded siNA molecule, and the second sequence further comprises a chemical moiety that can be used to isolate the bound oligonucleotide sequence; c) Using the chemical component of the second oligonucleotide sequence strand, isolate the full-length sequence containing both siNA oligonucleotide strands connected by a cleavable linker And purifying the product of (b) under conditions suitable for hybridization of the two siNA oligonucleotide strands to form a stable duplex. . In one embodiment, the cleavage of the linker molecule in (c) above is performed during the deprotection of the oligonucleotide, for example under hydrolysis conditions. In another embodiment, the cleavage of the linker molecule in (c) above is performed after deprotection of the oligonucleotide. In another embodiment, the method of synthesis includes solid phase synthesis on a solid support such as calibrated porous glass (CPG) or polystyrene, wherein the first sequence in (a) is a succinyl linker or the like. Synthesize on a cleavable linker using a solid support as a scaffold. The cleavable linker used as a scaffold for synthesizing the second strand in (a) is a solid such that the solid support derivatized linker and (a) cleavable linker are cleaved simultaneously or separately. It can have similar or different reactivity than the support derivatized linker. In one embodiment, the chemical moiety of (b) that can be used to isolate the bound oligonucleotide sequence comprises a trityl group, such as a dimethoxytrityl group.

In another aspect, the invention features a method of making a double stranded siNA molecule in a single synthetic process comprising: (a) oligonucleotide having a first sequence and a second sequence. Synthesizing, wherein the first sequence is complementary to the second sequence, the first oligonucleotide sequence is linked to the second sequence via a cleavable linker, and the second sequence The oligonucleotide having the sequence has a terminal 5′-protecting group, for example, 5′-O-dimethoxytrityl group (5′-O-DMT) remaining; (b) deprotecting the oligonucleotide; Cleaves the linker joining the two oligonucleotide sequences by deprotection; and (c) under conditions suitable for isolating double stranded siNA molecules, eg, trityl- On-synthesis With substantially comprises the step of, purifying the product of (b).

  In another embodiment, the method of synthesis of siNA molecules of the present invention is described in Scaringe et al., US Pat. Nos. 5,889,136; 6,008,400; and 6,111,086 (incorporated in its entirety). As cited herein).

  In one aspect, the invention features a siNA construct that mediates RNAi against HCV, wherein the siNA construct is one or more chemical modifications that increase the nuclease resistance of the siNA construct, eg, any of formulas I-VII Or one or more chemical modifications having any combination thereof.

  In another aspect, the invention features a method of generating a siNA molecule having increased nuclease resistance, the method comprising: (a) a nucleotide having any of formulas I-VII or any combination thereof And (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased nuclease resistance.

  In one aspect, the invention features a siNA construct that mediates RNAi to HCV, wherein the siNA construct modulates the binding affinity between the sense and antisense strands of the siNA construct, Including the chemical modifications described herein.

  In another aspect, the invention features a method of generating a siNA molecule having increased binding affinity between the sense and antisense strands of the siNA molecule, the method comprising: (a) Formula I Introducing nucleotides having any of VII or any combination thereof into siNA molecules and (b) siNA molecules with increased binding affinity between the sense and antisense strands of siNA molecules Assaying the siNA molecule of step (a) under conditions suitable for release.

  In one aspect, the invention features a siNA construct that mediates RNAi to HCV, wherein the siNA construct modulates the binding affinity between the antisense strand of the siNA construct and a complementary target RNA sequence in the cell. Including one or more chemical modifications described herein.

  In one aspect, the invention features an siNA construct that mediates RNAi to HCV, and the siNA construct modulates the binding affinity between the antisense strand of the siNA construct and a complementary target DNA sequence in the cell. Including one or more chemical modifications described herein.

  In another aspect, the invention features a method of generating a siNA molecule having increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence, the method comprising: ) Introducing nucleotides having any of formulas I-VII or any combination thereof into the siNA molecule, and (b) increasing the binding affinity between the antisense strand of the siNA molecule and the complementary target RNA sequence. Assaying the siNA molecule of step (a) under conditions suitable to identify the siNA molecule.

  In another aspect, the invention features a method of generating a siNA molecule having increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence, the method comprising: ) Introducing nucleotides having any of formulas I-VII or any combination thereof into the siNA molecule, and (b) increasing the binding affinity between the antisense strand of the siNA molecule and the complementary target DNA sequence. Assaying the siNA molecule of step (a) under conditions suitable for isolating said siNA molecule.

  In one aspect, the invention features a siNA construct that mediates RNAi to HCV, wherein the siNA construct is capable of producing additional endogenous siNA molecules that have sequence homology to a chemically modified siNA construct. It includes one or more chemical modifications described herein that modulate the polymerase activity of the sex polymerase.

  In another aspect, the present invention is directed to siNA capable of mediating an increase in the polymerase activity of a cellular polymerase that can generate additional endogenous siNA molecules having sequence homology to chemically modified siNA molecules. Characterized by a method for generating a molecule comprising: (a) introducing a nucleotide having any of formulas I-VII or any combination thereof into a siNA molecule; and (b) a chemically modified siNA. Under conditions suitable to isolate a siNA molecule capable of mediating an increase in the polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the molecule, step (a) Assaying a plurality of siNA molecules.

  In one aspect, the invention features a chemically modified siNA construct that mediates RNAi against HCV in a cell, wherein the chemical modification is the efficiency of RNAi mediated by such siNA construct. Does not significantly affect the interaction of siNA with target RNA molecules, DNA molecules and / or proteins or other factors essential to RNAi.

  In another aspect, the invention features a method of generating a siNA molecule having improved RNAi activity against HCV, the method comprising: (a) any of formulas I-VII or any combination thereof Introducing a nucleotide having a siNA molecule and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating a siNA molecule having improved RNAi activity.

  In yet another aspect, the invention features a method of generating a siNA molecule having improved RNAi activity against HCV target RNA, the method comprising (a) any of formulas I-VII or any of them And (b) assaying the siNA molecule of step (a) under conditions suitable for isolating a siNA molecule having improved RNAi activity against the target RNA. , Including that.

  In yet another aspect, the invention features a method of generating a siNA molecule having improved RNAi activity against HCV target DNA, the method comprising (a) any of formulas I-VII or any of them And (b) assaying the siNA molecule of step (a) under conditions suitable for isolating a siNA molecule having improved RNAi activity against the target DNA , Including that.

  In one aspect, the invention features a siNA construct that mediates RNAi against HCV, wherein the siNA construct modulates one or more chemistries described herein that modulate cellular uptake of the siNA construct. Including physical modification.

  In another aspect, the invention features a method of generating a siNA molecule against HCV having improved cellular uptake, the method comprising (a) any of formulas I-VII or any combination thereof Introducing the nucleotide having the siNA molecule and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating the siNA molecule having improved cellular uptake.

  In one aspect, the invention features a siNA construct that mediates RNAi against HCV, wherein the siNA construct is a polymer such as, for example, polyethylene glycol or equivalent conjugates that improve the pharmacokinetics of the siNA construct. As described herein, the bioavailability of siNA constructs is increased by conjugating a sex conjugate or by conjugating a conjugate that targets a specific tissue type or cell type in vivo. Or further chemical modifications. Non-limiting examples of such conjugates are described in Vargese et al. , US patent application Ser. No. 10 / 201,394, which is hereby incorporated by reference.

  In one aspect, the invention features a method of generating a siNA molecule of the invention having improved bioavailability, the method comprising: (a) introducing a conjugate into the structure of the siNA molecule; And (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules with improved bioavailability. Such conjugates include cell receptor ligands such as peptides derived from naturally occurring protein ligands; protein localization sequences such as cellular ZIP coding sequences; antibodies; nucleic acid aptamers; vitamins and other cofactors such as Folic acid and N-acetylgalactosamine; polymers such as polyethylene glycol (PEG); phospholipids; polyamines such as spermine or spermidine; and others.

  In another aspect, the invention features a method of generating a siNA molecule of the invention having improved bioavailability, the method comprising: (a) introducing an excipient formulation into the siNA molecule; and (B) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules with improved bioavailability. Such excipients include polymers such as cyclodextrins, lipids, cationic lipids, polyamines, phospholipids, and others.

  In another aspect, the invention features a method of generating a siNA molecule of the invention having improved bioavailability, the method comprising (a) any of formulas I-VII or any of them Introducing nucleotides having the combination into the siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating the siNA molecule with improved bioavailability. .

  In another embodiment, polyethylene glycol (PEG) can be covalently attached to the siNA compounds of the invention. The conjugated PEG can be of any molecular weight, preferably from about 2,000 to about 50,000 daltons (Da).

The present invention can be used alone or as a component of a kit having at least one of the reagents necessary to introduce RNA into a test sample and / or subject in vitro or in vivo. For example, preferred components of the kit include siNA molecules of the invention and vehicles that facilitate the introduction of siNA into the cell of interest as described herein (eg, lipids and the art Other transfection methods known in the art are used, for example, Beigelman et al, US Pat.
3). The kit can be used, for example, for target evaluation in the determination of gene function and / or activity, or in drug optimization, and in drug discovery (see, eg, Usman et al., US Patent Application 60/402, 996). Such a kit may also include guidance for enabling the user of the kit to practice the invention.

As used herein, “short interfering nucleic acid”, “siNA”, “short interfering RNA”, “siR”
The term “NA”, “short interfering nucleic acid molecule”, “short interfering oligonucleotide molecule”, or “chemically modified short interfering nucleic acid molecule” refers to, for example, RNA interference (“RNAi”) in a sequence-specific manner. Or any nucleic acid molecule that can down-regulate gene expression or viral replication by mediating gene silencing (eg, Bass, 2001, Nature, 411, 428-429; Elbashir et al., 2001, Nature, Kreutzer et al., International Publication WO 00/44895; Zernica-Goetz et al., International Publication WO 01/36646; Fire, International Publication WO 99/32619; Plaetinck et al., International Publication WO 00/01846; Mell and Fire, International Publication WO01 / 29058; Deschamps-Depallette, International Publication WO99 / 07409; and Li et al., International Publication WO00 / 44914; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002. Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237; Hutvagner and Zamore, 2002, Science, 297, 2056-60; McManus et al., 2002, RNA, 8, 842-850; Reinhart et al., 20 2, Gene & Dev., 16, 1616-1626; and Reinhart & Bartel, 2002, Science, 297, 1831.) Non-limiting examples of siNA molecules of the present invention are shown in Figures 4-6 and Tables II, III herein. And, for example, siNA may be a double-stranded polynucleotide molecule comprising self-complementary sense and antisense regions, where the antisense region is present in the target nucleic acid molecule or a portion thereof. The sense region has a nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, wherein the siNA can be assembled from two separate oligonucleotides, where one strand is The sense strand, the other is the antisense strand, and the antisense strand The strand and sense strand are self-complementary (ie, each strand contains a nucleotide sequence that is complementary to the nucleotide sequence in the other strand, eg, the antisense and sense strands have a duplex or double stranded structure. For example, the double-stranded region is about 19 base pairs); the antisense strand comprises a nucleotide sequence that is complementary to the nucleotide sequence in the target nucleic acid molecule or portion thereof, and the sense strand is the target nucleic acid sequence or its It includes a nucleotide sequence corresponding to a part. Alternatively, siNA may be assembled from a single oligonucleotide, where the self-complementary sense and antisense regions of siNA are linked by a nucleic acid based or non-nucleic acid based linker. The siNA may be a polynucleotide having a hairpin secondary structure having a self-complementary sense region and an antisense region, wherein the antisense region is complementary to a nucleotide sequence in another target nucleic acid molecule or part thereof. The sense region has a nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA may be a circular single-stranded polynucleotide having a stem comprising two or more loop structures and self-complementary sense and antisense regions, wherein the antisense region is a target nucleic acid molecule or a portion thereof Including a nucleotide sequence complementary to the nucleotide sequence therein, the sense region has a nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, and the circular polynucleotide can be processed in vivo or in vitro to mediate RNAi Active siNA molecules can be generated. The siNA may also include a single-stranded polynucleotide having a nucleotide sequence that is complementary to the nucleotide sequence in the target nucleic acid molecule or a portion thereof (eg, such siNA molecules are included in the target nucleic acid sequence in the siNA molecule). Or where there is no need for the presence of a nucleotide sequence corresponding to a portion thereof), where the single stranded polynucleotide is further linked to a terminal phosphate group, such as 5′-phosphate (eg, Martinez et al., 2002, Cell). , 110, 563-574 and Schwarz et al., 2002, Molecular Cell, 10, 537-568), or 5 ′, 3′-diphosphate. In some embodiments, the siNA molecules of the invention may contain separate sense and antisense sequences or regions, wherein the sense and antisense regions are covalently linked by nucleotide or non-nucleotide linker molecules known in the art. Or non-covalently linked by ionic, hydrogen, van der Waals, hydrophobic, and / or stacking interactions. In certain embodiments, the siNA molecules of the invention comprise a nucleotide sequence that is complementary to the nucleotide sequence of the target gene. In another embodiment, the siNA molecule of the invention interacts with the nucleotide sequence of the target gene such that inhibition of expression of the target gene is caused. As used herein, siNA molecules need not be limited to molecules containing only RNA, but also include chemically modified nucleotides and non-nucleotides. In certain embodiments, the short interfering nucleic acid molecules of the invention lack 2′-hydroxy (2′-OH) containing nucleotides. Applicants, in certain embodiments, describe short interfering nucleic acids that do not require the presence of a nucleotide having a 2′-hydroxy group to mediate RNAi. That is, the short interfering nucleic acid molecule of the present invention may not contain any ribonucleotide (for example, a nucleotide having a 2′-OH group). However, such siNA molecules that do not require the presence of ribonucleotides in the siNA molecule to support RNAi include one or more nucleotides having a 2′-OH group, a linked linker or other linkage Can have groups, components, or chains that are attached or associated. Optionally, the siNA molecule can include ribonucleotides at about 5, 10, 20, 30, 40, or 50% of the nucleotide positions. The modified short interference nucleic acid molecules of the present invention are also referred to as short interference modified oligonucleotide “siMON”. As used herein, the term siNA refers to other terms used to describe nucleic acid molecules that can mediate sequence-specific RNAi, such as short interfering RNA (siRNA), double-stranded RNA (dsRNA) , MicroRNA (miRNA), short hairpin RNA (shRNA), short interference oligonucleotide, short interference nucleic acid, short interference modified oligonucleotide, chemically modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others It is equivalent to the thing. Furthermore, as used herein, the term RNAi means equivalent to other terms describing sequence-specific RNA interference, such as post-transcriptional gene silencing or epigenetics. . For example, the siNA molecules of the invention can be used to epigenically silence genes both at the post-transcriptional level or at the pre-transcriptional level. In a non-limiting example, epigenetic control of gene expression by the siNA molecules of the present invention can be caused by siNA-mediated modification of chromatin structure to alter gene expression (eg, Allshire, 2002, Science, 297). Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237). .

  “Modulate” refers to the expression of a gene, or the level of an RNA molecule or equivalent RNA molecule encoding one or more proteins or protein subunits, or one or more activities of a protein or protein subunit, It means upregulated or downregulated such that expression, level, or activity is higher or lower than observed in the absence of modulator. For example, the term “modulate” can mean “inhibit”, but the use of the term “modulate” is not limited to this definition.

  “Inhibit” means that the activity of a gene expression product or the level of RNA encoding one or more gene products or equivalent RNA is reduced below that observed in the absence of the nucleic acid molecule of the present invention. Means. In one embodiment, inhibition by siNA molecules is preferably below the level observed in the presence of inactive or attenuated molecules that are unable to mediate RNAi responses. In another embodiment, inhibition of gene expression by the siNA molecules of the invention is greater in the presence of siNA molecules than in the absence.

  “Inhibit,” “down-regulate,” or “decrease” refers to gene expression, or the level of an RNA molecule that encodes one or more proteins or protein subunits or equivalent RNA molecules, or 1 It means that the activity of the protein or protein subunit or higher is reduced below that observed in the absence of the nucleic acid molecule of the invention (eg siNA). In one embodiment, inhibition, down-regulation or reduction by siNA molecules is below the level observed in the presence of inactive or attenuated molecules. In another embodiment, inhibition, down-regulation, or reduction by siNA molecules is below the level observed in the presence of, for example, siNA molecules with scrambled sequences or mismatches. In another embodiment, inhibition, downregulation, or reduction of gene expression by a nucleic acid molecule of the invention is greater in the presence of the nucleic acid molecule and in its absence.

  “Gene” or “target gene” means a nucleic acid that encodes an RNA, and includes, but is not limited to, a nucleic acid sequence such as a structural gene that encodes a polypeptide. The target gene can be a gene derived from a cell, an endogenous gene, transgin, or a foreign gene, such as a gene of a pathogen present in a cell after infection with a pathogen (eg, a virus). The cell containing the target gene can be derived from or contained within any organism, such as a plant, animal, protozoan, virus, bacterium or fungus. Non-limiting examples of plants include monocotyledons, dicotyledons, or gymnosperms. Non-limiting examples of animals include vertebrates or invertebrates. Non-limiting examples of fungi include filamentous fungi or yeast.

  As used herein, “HCV” means hepatitis C virus, or any protein, peptide or polypeptide having hepatitis C virus activity or encoded by the HCV genome. The term “HCV” also includes a nucleic acid molecule that encodes an RNA or protein that is associated with the development and / or maintenance of HCV infection, such as a nucleic acid molecule that encodes a polypeptide, including HCV RNA or a polypeptide of a different strain of HCV. (Eg, a polynucleotide having the Genbank accession number shown in Table I), mutant HCV genes, and splicing variants of HCV genes, and genes involved in the HCV pathway and / or HCV activity of gene expression. The term “HCV” is also meant to include HCV viral gene products and genes that regulate cellular targets of HCV infection, such as those described herein.

  “HCV protein” means a protein, peptide or polypeptide having hepatitis C virus activity or encoded by the HCV genome.

  “Highly conserved sequence region” means that the nucleotide sequence of one or more regions in a target gene is one generation and another generation, or one biological system and another biological It means that there is no significant difference with the system.

  “Sense region” means a nucleotide sequence of a siNA molecule having complementarity to the antisense region of the siNA molecule. Furthermore, the sense region of the siNA molecule can include a nucleic acid sequence having homology with the target nucleic acid sequence.

  “Antisense region” means the nucleotide sequence of a siNA molecule having complementarity to a target nucleic acid sequence. Furthermore, the antisense region of the siNA molecule can optionally include a nucleic acid sequence having complementarity to the sense region of the siNA molecule.

  “Target nucleic acid” means any nucleic acid sequence whose expression or activity is to be regulated. The target nucleic acid can be DNA or RNA.

“Complementarity” means that nucleic acids can form hydrogen bonds with another nucleic acid sequence, either by traditional Watson-Crick or other non-traditional types. With respect to the nucleic acid molecules of the present invention, the free energy of binding between the nucleic acid molecule and its complementary sequence is sufficient to drive the appropriate function of the nucleic acid, eg, RNAi activity. Determination of binding free energy for nucleic acid molecules is well known in the art (eg, Turner et al.
al. , 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al, 1986, Proc. Nat. Acad. Sci. USA 83: 9373-9377; Turner et al. , 1987, J. et al. Am. Chem. Soc. 109: 3783-3785). The percentage of complementarity indicates the percentage of consecutive residues in a nucleic acid molecule that can form hydrogen bonds (eg, Watson-Crick base pairing) with a second nucleic acid sequence (eg, 5 in 10 bases). 6,7.8,9,10 bases are 50%, 60%, 70%, 80%, 90%, and 100% complementarity). “Complete complementarity” means that all consecutive residues of a nucleic acid sequence will hydrogen bond with the same number of consecutive residues in a second nucleic acid sequence.

  The siNA molecules of the present invention are intended to treat various diseases and conditions such as HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, and any other indication that may be responsive to the level of HCV in cells or tissues. It is a new treatment method.

  In one embodiment of the invention, each sequence of the siNA molecule of the invention is independently about 18 to about 24 nucleotides in length, and in certain embodiments about 18, 19, 20, 21, It is 22, 23, or 24 nucleotides in length. In another embodiment, the siNA duplex of the invention independently comprises about 17 to about 23 (eg, about 17, 18, 19, 20, 21, 22, or 23) base pairs. In yet another embodiment, siNA molecules of the invention comprising hairpins or cyclic structures are about 35 to about 55 (eg, about 35, 40, 45, 50 or 55) nucleotides in length, or about 38 -About 44 (eg 38, 39, 40, 41, 42, 43 or 44) nucleotides in length and about 16 to about 22 (eg about 16, 17, 18, 19, 20, 21 or 22). Contains base pairs. Exemplary siNA molecules of the invention are shown in Table II. Exemplary synthetic siNA molecules of the invention are shown in Tables III and IV, and / or FIGS. 4-5.

  As used herein, “cell” is used in its normal biological sense and does not refer to an entire multicellular organism, particularly to a human. Cells can be present in living organisms, for example, birds, plants and mammals such as humans, cows, goats, tailless monkeys, tailed monkeys, pigs, dogs and cats. The cell may be prokaryotic (eg, a bacterial cell) or eukaryotic (eg, a mammalian or plant cell). The cell may be of somatic or germline origin, may be totipotent or pluripotent, and may or may not divide. The cells may also be derived from or contain gametes or embryos, stem cells, or fully differentiated cells.

The siNA molecules of the present invention may be added directly or complexed with a cationic lipid, encapsulated in liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complex can be administered locally to the relevant tissue ex vivo or in vivo using an injection, infusion pump or stent, with or without incorporation into the biopolymer. In certain embodiments, the nucleic acid molecules of the invention comprise the sequences shown in Table II-III and / or FIGS. 4-5. Examples of such nucleic acid molecules consist essentially of the sequences defined in these tables and drawings. In addition, the chemically modified constructs described in Table IV can be applied to any siNA sequence of the invention.

  In another aspect, the present invention provides a mammalian cell comprising one or more siNA molecules of the present invention. One or more siNA molecules can independently target the same or different sites.

“RNA” means a molecule comprising at least one ribonucleotide residue. “Ribonucleotide” means a nucleotide having a hydroxyl group at the 2 ′ position of a β-D-ribofuranose component. The term includes double-stranded RNA, single-stranded RNA, isolated RNA, such as partially produced RNA, essentially pure RNA, synthetic RNA, recombinantly produced RNA, and 1 Or RNA that has been altered to differ from naturally occurring RNA by addition, deletion, substitution and / or alteration of more nucleotides. Such alterations can include the addition of non-nucleotide material, eg, addition to the end or interior of siNA (eg, at least one or more nucleotides of RNA). Nucleotides in the RNA molecules of the invention can also include non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally occurring RNA.

  “Subject” means an organism or cell itself that is a donor or recipient of explanted cells. “Subject” also refers to an organism that can be administered a nucleic acid molecule of the invention. In one embodiment, the subject is a mammal or a mammalian cell. In another embodiment, the subject is a human or human cell.

  As used herein, the term “phosphorothioate” refers to an internucleotide linkage having the formula I, wherein Z and / or W includes a sulfur atom. Thus, the term phosphorothioate refers to both phosphorothioate and phosphorodithioate internucleotide linkages.

  As used herein, the term “universal base” refers to each of the natural DNA / RNA bases and nucleotide base analogs that form base pairs with little discrimination between them. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatics, as known in the art (see, for example, Loakes, 2001, Nucleic Acids Research, 29, 2437-2447). Derivatives, inosine, azolecarboxamide, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole.

  As used herein, the term “acyclic nucleotide” refers to any nucleotide having an acyclic ribose sugar, such as any of the ribose carbons (C1, C2, C3, C4, or C5). Or in combination represents a nucleotide that is not present in the nucleotide.

The nucleic acid molecules of the invention can be used to treat the diseases or conditions described herein, either individually or in combination with other agents (eg, the siRNA molecules of the invention For example, it can be adapted for use to treat HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, and other indications that may be responsive to levels of HCV in cells or tissues). For example, to treat a particular disease or condition, siNA molecules can be administered to a subject individually or in combination with one or more agents under conditions suitable for treatment, or will be apparent to those of skill in the art It can be administered to other suitable cells.

  In yet another embodiment, siNA molecules can be used in combination with other known therapies to treat the aforementioned health conditions or diseases. For example, the molecules described herein can be used in combination with one or more known therapeutic agents to treat a disease or condition. Non-limiting examples of other therapeutic agents that can be readily combined with the siNA molecules of the invention include enzymatic nucleic acid molecules, allosteric nucleic acid molecules, antisense, decoy, or aptamer nucleic acid molecules, antibodies such as monoclonal antibodies, small molecules , And other organic and / or inorganic compounds such as metals, salts and ions.

  In one aspect, the invention features an expression vector that includes a nucleic acid sequence encoding at least one siNA molecule of the invention so as to allow expression of the siNA molecule. For example, a vector can include sequences that encode both strands of a siNA molecule including the duplex. The vector can also include a sequence encoding one nucleic acid molecule that is self-complementary and thus forms a siNA molecule. Non-limiting examples of such expression vectors are described by Paul et al. , 2002, Nature Biotechnology, 19, 505; Miyagi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al. , 2002, Nature Biotechnology, 19,500; and Novina et al. , 2002, Nature Medicine, advance online publication doi: 10.1038 / nm725.

  In another aspect, the invention features a mammalian cell, eg, a human cell, comprising the expression vector of the invention.

  In yet another embodiment, the expression vector of the invention comprises a sequence of siNA molecules having complementarity to the RNA molecule represented by the Genbank accession number, eg, the Genbank accession number shown in Table I.

  In one embodiment, the expression vector of the invention comprises a nucleic acid sequence encoding two or more siNA molecules, which may be the same or different.

In another aspect of the invention, a siNA molecule that interacts with a target RNA molecule and down-regulates a gene that encodes the target RNA molecule (eg, a target RNA molecule represented herein by a Genbank accession number). Is expressed from a transcription unit inserted into a DNA or RNA vector. The recombinant vector can be a DNA plasmid or a viral vector. Viral vectors expressing siNA can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. Recombinant vectors capable of expressing siNA molecules are delivered as described herein and remain in the target cells. Alternatively, viral vectors that provide transient expression of siNA molecules can be used. Such vectors can be repeatedly administered as necessary. Once expressed, siNA molecules bind and down-regulate gene function or expression by RNA interference (RNAi). Delivery of vectors expressing siNA can be systemic (eg, by intravenous or intramuscular administration)
Administration to target cells explanted from a subject, followed by reintroduction into the subject, or any other means that allows introduction into the desired target cells.

  By “vector” is meant any nucleic acid and / or virus-based procedure used to deliver a desired nucleic acid.

  Other features and advantages of the invention will be apparent from the following description of preferred embodiments of the invention and from the claims.

FIG. 1 shows an example of a scheme for synthesizing siNA molecules. FIG. 2 shows MALDI-TOV mass spectrometry of purified siNA duplex synthesized by the method of the present invention. FIG. 3 is a diagram showing an example of a proposed mechanism of target RNA degradation involved in RNAi. FIG. 4 shows an example of a chemically modified siNA construct. FIG. 5 shows an example of a specific siNA sequence that has been chemically modified. FIG. 6 shows examples of various siNA constructs. FIG. 7 is a schematic diagram of the scheme used to create an expression cassette for generating siNA hairpin constructs. FIG. 8 is a schematic diagram of a scheme used to create an expression cassette to generate a double stranded siNA construct. FIG. 9 is a schematic diagram of the method used to determine a particular target nucleic acid sequence. FIG. 10 shows examples of various stabilization chemistries that can be used to stabilize the 3 'end of the siNA sequence. FIG. 11 shows an example of a strategy used to identify chemically modified siNA constructs. FIG. 12 shows a non-limiting example of a siRNA construct targeting viral replication of an HCV / poliovirus chimera. FIG. 13 shows a non-limiting example of an siRNA construct targeting viral replication of an HCV / poliovirus chimera. FIG. 14 shows a non-limiting example of a chemically modified siRNA construct targeting viral replication of an HCV / poliovirus chimera. FIG. 15 shows a non-limiting example of a chemically modified siRNA construct targeting viral replication of an HCV / poliovirus chimera. FIG. 16 shows a non-limiting example of treatment with several chemically modified siRNA constructs that target viral replication of HCV / poliovirus chimeras. FIG. 17 shows a non-limiting example of treatment with several chemically modified siRNA constructs that target viral replication of HCV / poliovirus chimeras. FIG. 18 shows a non-limiting example of treatment with several chemically modified siRNA constructs that target viral replication of the Huh7 HCV replicon system.

BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 shows a non-limiting example of a scheme for synthesizing siNA molecules. The complementary siNA sequence strands strand 1 and strand 2 are synthesized in tandem and joined with cleavable linkages, such as nucleotide succinates or abasic succinates. This may be the same as or different from the cleavable linker used in the solid phase synthesis on the solid support. The synthesis may be solid phase or liquid phase, and in the example shown, the synthesis is solid phase synthesis. The synthesis is performed so that a protecting group such as a dimethoxytrityl group remains on the terminal nucleotide of the tandem oligonucleotide. When the oligonucleotide is cleaved and deprotected, the two siNA strands spontaneously hybridize to form a siNA duplex, so that the duplex can be purified using the properties of the terminal protecting group. This can be done, for example, by applying a tritylone purification method in which only duplex / oligonucleotides with terminal protecting groups are isolated.

  FIG. 2 shows MALDI-TOV mass spectrometry of purified siNA duplex synthesized by the method of the present invention. The two peaks shown correspond to the estimated mass of separate siNA sequence chains. This result indicates that the siNA duplex generated from tandem synthesis can be purified as a single substance using simple tritylone purification methodology.

  FIG. 3 is a diagram showing a non-limiting example of a proposed mechanism of target RNA degradation involved in RNAi. A double-stranded RNA (dsRNA) generated by an RNA-dependent RNA polymerase (RdRP) from a foreign single-stranded RNA, such as a virus, transposon, or other exogenous RNA, activates the Dicer enzyme, and then This creates a siNA duplex. Alternatively, synthesized or expressed siNA can be introduced directly into cells by any suitable means. An active siNA complex is formed, which recognizes the target RNA, resulting in degradation of the target RNA by the RISC endonuclease complex or synthesis of additional RNA by RNA-dependent RNA polymerase (RdRP). , Which activates Dicer to produce additional siNA molecules, which amplify the RNAi response.

  4A-F show non-limiting examples of chemically modified siNA constructs of the invention. In the figure, N represents any nucleotide (adenosine, guanine, cytosine, uridine, or optionally thymidine), and for example, it may be substituted with thymidine in the overhang region represented by parentheses (NN). Various modifications have been shown for the sense and antisense strands of the siNA construct.

FIG. 4A: The sense strand contains 21 nucleotides with 4 phosphorothioate 5′- and 3 ′ terminal internucleotide linkages, where the two terminal 3′-nucleotides may optionally be base-paired and present All possible pyrimidine nucleotides are 2′-O-methyl or 2′-deoxy-2′-fluoro modified nucleotides except (NN) nucleotides, which are ribonucleotides, deoxynucleotides, universal bases, or Other chemical modifications described can be included. The antisense strand may comprise 21 nucleotides and optionally have a 3 ′ terminal glyceryl component, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence; It may have one 3 ′ terminal phosphorothioate internucleotide linkage and four 5 ′ terminal phosphorothioate internucleotide linkages, and all possible pyrimidine nucleotides may be 2′-deoxy-2 ′ except (NN) nucleotides. A fluoro-modified nucleotide, which can include ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications as described herein.

  FIG. 4B: The sense strand contains 21 nucleotides, where the two terminal 3′-nucleotides may optionally be base-paired, and all pyrimidine nucleotides that may be present are 2 ′ except (NN) nucleotides. -O-methyl or 2'-deoxy-2'-fluoro modified nucleotides, which can include ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand may comprise 21 nucleotides and optionally have a 3 ′ terminal glyceryl moiety, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence. All pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except (NN) nucleotides, which are ribonucleotides, deoxynucleotides, universal bases, or other Chemical modifications can be included.

  FIG. 4C: The sense strand contains 21 nucleotides with a 5 ′ end cap component and a 3 ′ end cap component, where the two terminal 3′-nucleotides are optionally base-paired and may be present All pyrimidine nucleotides are 2′-O-methyl or 2′-deoxy-2′-fluoro modified nucleotides except (NN) nucleotides, which are ribonucleotides, deoxynucleotides, universal bases, or as described herein. Other chemical modifications may be included. The antisense strand may comprise 21 nucleotides and optionally have a 3 ′ terminal glyceryl moiety, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence. , Which may have one 3 ′ terminal phosphorothioate internucleotide linkage, and all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except (NN) nucleotides, which are Nucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein can be included.

  FIG. 4D: The sense strand comprises 21 nucleotides with a 5 ′ end cap component and a 3 ′ end cap component, where the two terminal 3′-nucleotides may optionally be base-paired and all present The pyrimidine nucleotides of this are 2′-deoxy-2′-fluoro modified nucleotides, except for (NN) nucleotides, which contain ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. All purine nucleotides that can be present are 2'-deoxynucleotides. The antisense strand contains 21 nucleotides, which may optionally have a 3 ′ terminal glyceryl moiety, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence. Well, it may have a single 3 ′ terminal phosphorothioate internucleotide linkage, all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides, and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except (NN) nucleotides, which can include ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein.

FIG. 4E: The sense strand contains 21 nucleotides with a 5 ′ end cap component and a 3 ′ end cap component, where the two terminal 3′-nucleotides may optionally be base-paired and all present The pyrimidine nucleotides, except for (NN) nucleotides, are 2′-deoxy-2′-fluoro modified nucleotides, which are ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. Can be included. The antisense strand may comprise 21 nucleotides and optionally have a 3 ′ terminal glyceryl component, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence; All pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides, and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except (NN) nucleotides, Ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein can be included.

  FIG. 4F: The sense strand contains 21 nucleotides with a 5 ′ end cap component and a 3 ′ end cap component, where the two terminal 3′-nucleotides may optionally be base-paired and all present The pyrimidine nucleotides of this are 2′-deoxy-2′-fluoro modified nucleotides, except for (NN) nucleotides, which contain ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. be able to. The antisense strand may comprise 21 nucleotides and optionally have a 3 ′ terminal glyceryl component, where the two terminal 3′-nucleotides may optionally be complementary to the target RNA sequence; It may have one 3 ′ terminal phosphorothioate internucleotide linkage, all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides, and all purine nucleotides that may be present are (NN 2) -deoxynucleotides except for nucleotides, which can include ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand of construct AF includes a sequence that is complementary to any target nucleic acid sequence of the present invention.

  5A-F show non-limiting examples of specific chemically modified siNA sequences of the invention. A-F is obtained by applying the chemical modification shown in FIGS. 4A-F to the HCV siNA sequence.

  FIG. 6 shows non-limiting examples of various siNA constructs of the present invention. The examples shown (Constructs 1, 2, and 3) have a typical 19 base pairs, but different embodiments of the invention include any number of base pairs described herein. The region in parenthesis represents a nucleotide overhang containing, for example, about 1, 2, 3, or 4 nucleotides in length, preferably about 2 nucleotides. Constructs 1 and 2 can be used independently for RNAi activity. Construct 2 can include a polynucleotide or non-nucleotide linker, which can optionally be designed as a biodegradable linker. In one embodiment, the loop structure shown in Construct 2 can include a biodegradable linker, thereby forming Construct 1 in vivo and / or in vitro. In another example, construct 3 can be used to generate construct 2 on the same principle, where the linker is used to generate siNA construct 2 that is active in vivo and / or in vitro, Optionally, another biodegradable linker can be used to generate siNA construct 1 that is active in vivo and / or in vitro. As such, the stability and / or activity of the siNA construct can be modulated based on the design of the siNA construct for use in vivo or in vitro, and / or in vitro.

  FIGS. 7A-C are schematic diagrams of schemes used to create expression cassettes for generating siNA hairpin constructs.

FIG. 7A: A DNA oligomer is synthesized to include a 5′-restriction site (Rl) sequence, followed by a region having the same sequence as the predetermined HCV target sequence (siNA sense region). Wherein the sense region is, for example, a loop sequence of defined sequence (X) having a length of about 19, 20, 21, or 22 nucleotides (N) followed by, for example, about 3 to about 10 nucleotides Have

  7B: The synthetic construct is then extended with DNA polymerase to produce a hairpin structure having a self-complementary sequence, thereby having specificity for the HCV target sequence and having a self-complementary sense region and an antisense region. SiNA transcripts having are obtained.

  FIG. 7C: Heating the construct (eg, to about 95 ° C.) to linearize the sequence, so that a complementary second strand of DNA is obtained using a primer for the 3′-restriction sequence of the first strand. Can stretch. The double stranded DNA is then inserted into an appropriate vector for expression in the cell. Constructs can be 3 ′ by transcription, for example, by designing restriction sites and / or utilizing the poly-U-terminal region as described in Paul et al. (2002, Nature Biotechnology, 29, 505-508). It can be designed to produce a terminal nucleotide overhang.

  FIGS. 8A-C are schematic diagrams of schemes used to create expression cassettes to generate double stranded siNA constructs.

  FIG. 8A: A DNA oligomer is synthesized to have a 5'-restriction (R1) site sequence and then a region (siNA sense region) having the same sequence as the predetermined HCV target sequence. Here, the sense region includes, for example, a length of about 19, 20, 21, or 22 nucleotides (N), followed by a 3′-restriction site (R2) adjacent to the loop sequence of defined sequence (X) ).

  FIG. 8B: The synthetic construct is then extended with DNA polymerase to produce a hairpin structure with a self-complementary sequence.

  FIG. 8C: The construct is treated with restriction enzymes specific for R1 and R2 to produce double stranded DNA, which is then inserted into a suitable vector for expression in cells. The transcription cassette is designed so that the U6 promoter region sandwiches both sides of the dsDNA, thereby producing separate sense and antisense strands of siNA. A poly T-terminal sequence can be added to the construct to generate a U overhang in the resulting transcript.

  FIGS. 9A-E are schematic diagrams of the methods used to determine the target site of siNA-mediated RNAi in a particular target nucleic acid sequence, eg, messenger RNA.

  FIG. 9A: A pool of siNA oligonucleotides is synthesized so that the antisense region of the siNA construct has complementarity to the target site throughout the target nucleic acid sequence, and the sense region includes a sequence complementary to the antisense region of siNA. .

  9B and C: The sequences are pooled and inserted into the vector (FIG. 9B) so that siNA is expressed by transfection of the vector into the cells (FIG. 9C).

  FIG. 9D: Sort cells based on phenotypic changes associated with modulation of target nucleic acid sequence.

  FIG. 9E: siNA is isolated from sorted cells and sequenced to identify valid target sites in the target nucleic acid sequence.

  FIG. 10 shows, for example, non-limiting examples of various stabilization chemistries (1-10) that can be used to stabilize the 3 ′ end of the siNA sequences of the present invention: (1) [3- 3 ']-inverted deoxyribose; (2) deoxyribonucleotides; (3) [5'-3']-3'-deoxyribonucleotides; (4) [5'-3 ']-ribonucleotides; (5) [5 '-3']-3'-O-methylribonucleotide; (6) 3'-glyceryl; (7) [3'-5 ']-3'-deoxyribonucleotide; (8) [3'-3'] Deoxyribonucleotides; (9) [5′-2 ′]-deoxyribonucleotides; and (10) [5-3 ′]-dideoxyribonucleotides. In addition to the modified and unmodified backbone chemistry shown in the drawings, these chemistries can be combined with other backbone modifications as described herein, eg, backbone modifications having Formula I. Furthermore, the 2′-deoxynucleotides shown 5 ′ to the terminal modifications shown may be another modified or unmodified nucleotide or non-nucleotide as described herein, eg, Formula I-VII or any combination thereof It may be a modification having

  FIG. 11 shows a non-limiting example of a strategy used to identify chemically modified siNA constructs of the invention that are resistant to nucleases but retain the ability to mediate RNAi activity. Chemical modifications are introduced into siNA constructs based on experience-based design parameters (eg, introduction of 2'-modifications, base modifications, backbone modifications, end cap modifications, etc.). The modified construct is tested in an appropriate system (eg, human serum for nuclease resistance, or an animal model for PK / delivery parameters as indicated). In parallel, siNA constructs are tested for RNAi activity, eg, in a cell culture system, eg, by a luciferase reporter assay. A lead siNA construct with specific characteristics but retaining RNAi activity is then identified, further modified and assayed again. This same method can be used to identify siNA-conjugated molecules with improved pharmacokinetic profile, delivery, and RNAi activity.

  FIG. 12 shows non-limiting examples of siRNA constructs 29579/29586 and 29578/29585 targeting viral replication of HCV / poliovirus chimeras compared to the inverted siNA control construct 29593/29600.

  FIG. 13 shows a non-limiting example of a dose response experiment of siRNA construct 29579/29586 targeting viral replication of HCV / poliovirus chimeras compared to the inverted siNA control construct 29593/29600. Inhibition of HCV / poliovirus chimera replication by the 29579/29586 siNA construct was measured with 29579/29586 siNA constructs at 1 nM, 5 nM, 10 nM, and 25 nM concentrations.

  FIG. 14 shows a non-limiting example of a chemically modified siRNA construct 30051/30053 targeting viral replication of an HCV / poliovirus chimera compared to the inverted siNA control construct 30052/30054.

  FIG. 15 shows a non-limiting example of a chemically modified siRNA construct 30055/30057 targeting viral replication of an HCV / poliovirus chimera compared to the inverted siNA control construct 30056/30058.

  FIG. 16 shows a non-limiting example of treatment with 10 nM of several chemically modified siRNA constructs targeting viral replication of HCV / poliovirus chimeras with lipid control and inverted siNA control constructs 29593/29600. Shown in comparison.

  FIG. 17 shows a non-limiting example of treatment with 25 nM of several chemically modified siRNA constructs targeting viral replication of HCV / poliovirus chimeras, lipid control and inverted siNA control constructs 29593/29600. Shown in comparison.

  FIG. 18 shows a non-limiting example of treatment of several chemically modified siRNA constructs targeting the viral replication of the Huh7 HCV replicon system at 25 nM with untreated cells (“cells”), lipofectamine (“ Shown compared to cells transfected with LFA2K ") and inverted siNA control constructs.

Detailed Description of the Invention
Mechanism of Action of the Nucleic Acid Molecules of the Invention The following discussion describes the proposed mechanism of RNA interference mediated by the currently known short interfering RNA, but is not meant to be limiting and is prior art It does not admit. Applicants anticipate herein that chemically modified short interfering nucleic acids have similar or improved RNAi-mediated ability to siRNA molecules and have improved stability and activity in vivo. Indicates that Therefore, this argument does not mean that it is limited to siRNA, and can be applied to the entire siNA. "RN
“Improved ability to mediate Ai” or “improved RNAi activity” means to include RNAi activity measured in vitro and / or in vivo, where RNAi activity mediates RNAi by siNA Reflects both the ability and stability of the siNA of the invention, where the product of these activities is compared in vitro and / or in vivo compared to total RNA siRNA or siNA containing multiple ribonucleotides. In some cases, the activity or stability of the siNA molecule may be reduced (ie, 1/10 or less), but the overall activity of the siNA molecule is enhanced in vitro and / or in vivo. .

  RNA interference refers to the process of sequence-specific post-transcriptional gene silencing mediated by short interfering RNA (siRNA) in animals (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and in fungi also referred to as querying. The post-transcriptional gene silencing process is thought to be an evolutionarily conserved cellular defense mechanism used to prevent the expression of foreign genes, and has different plexus and gates in common ( Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression is achieved by homologous single-stranded RNA or viral genomic RNA in response to the generation of double-stranded RNA (dsRNA) resulting from viral infection or random integration of transposon elements into the host genome. It may have evolved by a cellular response that specifically destroys. The presence of dsRNA in cells triggers an RNAi response by a mechanism that has not yet been fully characterized. This mechanism appears to be different from the interferon response, which results in nonspecific cleavage of mRNA by ribonuclease L as a result of dsRNA-mediated activation of protein kinases PKR and 2 ', 5'-oligoadenylate synthetase.

The presence of long dsRNA in the cell stimulates the activity of a ribonuclease III enzyme called Dicer. Dicer is involved in processing dsRNA into short fragments of dsRNA known as short interfering RNA (siRNA) (Berstein et al., 2001, Nature, 409, 363). Short interfering RNA resulting from Dicer activity is typically about 21-23 nucleotides in length and contains a duplex of about 19 base pairs. Dicer is also a small transient RNA of 21 and 22 nucleotides (s) from a conserved precursor RNA that has been implicated in translational control.
It has been suggested to be involved in excision of (tRNA) (Hutvagner et
al. , 2001, Science, 293,834). The RNAi response is also characterized by an endonuclease complex containing siRNA, commonly referred to as the RNA-induced silencing complex (RISC), which mediates the cleavage of single-stranded RNA having a sequence homologous to the siRNA . Cleavage of the target RNA occurs in the middle of the region complementary to the guide sequence of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188). Furthermore, RNA interference may involve gene silencing mediated by small RNAs (eg, microRNA or miRNA). This is probably due to a cellular mechanism that controls chromatin structure, which interferes with transcription of the target gene sequence (eg, Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002). , Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237). Thus, siNA molecules of the invention can be used to mediate gene silencing through interaction with RNA transcripts or through interaction with specific gene sequences, and Action results in gene silencing at either the transcriptional or post-transcriptional level.

  RNAi has been studied in various systems. Fire et al. (1998, Nature, 391, 806) is a C.I. RNAi was first observed in Elegans. Wianny and Goetz (1999, Nature Cell Biol., 2, 70) describe RNAi mediated by dsRNA in mouse embryos. Hammond et al. (2000, Nature, 404, 293) describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al. (2001, Nature, 411, 494) describe RNAi induced by introducing synthetic 21 nucleotide RNA duplexes in cultured mammalian cells such as human embryonic kidney cells and HeLa cells. Recent studies in Drosophila embryo lysates have revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies showed that the 21 nucleotide siRNA duplex was most active when it contained two 2 nucleotide 3 'terminal nucleotide overhangs. Furthermore, substitution of one or both siRNA strands with 2′-deoxy or 2′-O-methyl nucleotides destroys RNAi activity, but substitution of 3 ′ terminal siRNA nucleotides with deoxynucleotides is permissible. Indicated. A mismatch sequence in the center of the siRNA duplex has also been shown to disrupt RNAi activity. Furthermore, these studies also showed that the position of the cleavage site in the target RNA is defined by the 5 ′ end rather than the 3 ′ end of the siRNA guide sequence (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have shown that the 5'-phosphate of the target complement of the siRNA duplex is required for siRNA activity and that ATP is used to maintain the 5'-phosphate component of the siRNA (Nykanen et al. al., 2001, Cell, 107, 309), siRNA deficient in 5′-phosphate is active when introduced externally, which results in 5′-phosphorylation of the siRNA construct in vivo. Suggest that you may have.

Synthesis of nucleic acid molecules The synthesis of nucleic acids longer than 100 nucleotides is difficult using automated methods, and the therapeutic costs of such molecules are very high. In the present invention, preferably a small nucleic acid motif (“small” means a nucleic acid motif having a length of 100 nucleotides or less, preferably 80 nucleotides or less, most preferably 50 nucleotides or less, eg Of siNA oligonucleotide sequences or tandem synthesized siNA sequences) are used for external delivery. Since these molecules are simple in structure, the ability of nucleic acids to enter target regions of protein and / or RNA structures is high. The exemplary molecules of the present invention are chemically synthesized, but other molecules can be synthesized as well.

Oligonucleotides (eg, some modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides) are described, for example, in Caruthers et al. , 1992, Methods in Enzymology 211, 3-19, Thompson et al. , WO 99/54459, Wincott et al. , 1995, Nucleic Acids Res. 23, 2677-2684, Wincott et al. , 1997, Methods Mol. Bio. 74, 59, Brennan et al. , 1998, Biotechnol Bioeng. , 61, 33-45, and Brennan, US Pat. No. 6,001,311, which are synthesized using protocols known in the art (all of which are hereby incorporated by reference). To quote). Oligonucleotides are synthesized using common nucleic acid protecting groups and coupling groups such as dimethoxytrityl at the 5 ′ end and phosphoramidite at the 3 ′ end. In a non-limiting example, 394 Applied Biosystems, Inc. In a synthesizer, on a 0.2 μmol scale protocol, a 2.5 minute coupling step for 2′-O-methylated nucleotides and for 2′-deoxynucleotides or 2′-deoxy-2′-fluoronucleotides A small-scale synthesis is performed in a 45-second coupling process. Table V outlines the amount of reagents used in the synthesis cycle and the contact time. Alternatively, synthesis at the 0.2 μmol scale can be performed on a 96-well plate synthesizer, such as an apparatus manufactured by Protogene (Palo Alto, Calif.) With minimal modification to the cycle. In each coupling cycle of 2′-O-methyl residues, a 33-fold excess (60 μL of 0.11 M = 6.6 μmol) of 2′-O-methyl phosphoramidite and 5′-hydroxyl of polymer bound and A 105-fold excess of S-ethyltetrazole (60 μL of 0.25M = 15 μmol) can be used. In each coupling cycle of deoxy residues, a 22-fold excess (40 μL of 0.11 M = 4.4 μmol) deoxyphosphoramidite and a 70-fold excess of S-ethyltetrazole (40 μL) relative to the polymer-bound 5′-hydroxyl. 0.25 M = 10 μmol) can be used. 394 Applied Biosystems, Inc. The average coupling yield in the synthesizer is typically 97.5-99% as determined by colorimetric determination of the trityl fraction. 394 Applied Biosystems, Inc. Other oligonucleotide synthesis reagents used in the synthesizer are as follows: the detritylated solution is 3% TCA (ABI) in methylene chloride;
Capping is performed in 16% N-methylimidazole (ABI) in THF and 10% acetic anhydride / 10% 2,6-lutidine (ABI) in THF; the oxidizing solution is 16.9 mM I ₂ , 49 mM pyridine in THF. , 9% water (PERSEPTIVE®). Burdick & Jackson synthetic grade acetonitrile is used directly from the reagent bottle. S-ethyltetrazole solution (0.25 M in acetonitrile) was obtained from American International Chemical, Inc. Create from solids obtained from. Alternatively, a borage reagent (3H-1,2-benzodithiol-3-one 1,1-dioxide, 0.05M in acetonitrile) is used for introduction of phosphorothioate linkages.

Deprotection of the DNA-based oligonucleotide is performed as follows: Transfer the polymer-bound trityl-on-oligoribonucleotide to a 4 mL glass screw cap vial and suspend in a solution of 40% aqueous methylamine (1 mL) at 65 ° C. for 10 minutes. To do. After cooling to -20 ° C, the supernatant is removed from the polymer support. The support was added to 1.0 mL EtOH: MeCN: H ₂ O / 3: 1:
Wash three times with 1 and vortex, then add the supernatant to the first supernatant. The combined supernatant containing oligoribonucleotides is dried to obtain a white powder.

Synthetic methods used for RNA containing certain siNA molecules of the present invention are described by Usman et al. (1987 J. Am. Chem. Soc., 109, 7845), Scaringe et al. (1990 Nucleic Acids Res., 18, 5433) and According to the method described in Wincott et al. (1995 Nucleic Acids Res. 23, 2677-2684), Wincott et al. (1997, Methods Mol. Bio., 74, 59), conventional nucleic acid protecting groups and coupling groups such as 5 Performed with dimethoxytrityl at the 'terminal and phosphoramidite at the 3' terminal. In a non-limiting example, small scale synthesis is performed at 394 Applied Biosystems, Inc. Using a modified 0.2 μmol scale protocol on the synthesizer, a 7.5 minute coupling step for alkylsilyl protected nucleotides and a 2.5 minute coupling step for 2′-O-methylated nucleotides I do. Table V outlines the amount of reagents used in the synthesis cycle and the contact time. Alternatively, synthesis at the 0.2 μmol scale can be performed on a 96-well plate synthesizer, such as an apparatus manufactured by Protogene (Palo Alto, Calif.) With minimal modification to the cycle. In each coupling cycle of 2′-O-methyl residues, a 33-fold excess (60 μL of 0.11 M = 6.6 μmol) of 2′-O-methyl phosphoramidite and 5′-hydroxyl of polymer bound and A 75-fold excess of S-ethyltetrazole (60 μL of 0.25M = 15 μmol) can be used. In each coupling cycle of riboresidues, a 66-fold excess (120 μL 0.11 M = 13.2 μumol) alkylsilyl (ribo) protected phosphoramidite and 150-fold excess S relative to the polymer-bound 5′-hydroxyl. -Ethyltetrazole (120 [mu] L of 0.25 M = 30 [mu] mol) can be used. 394 Applied Biosystems, Inc. The average coupling yield in the synthesizer is typically 97.5-99% as determined by colorimetric determination of the trityl fraction. 394 Applied Biosystems, Inc. Other oligonucleotide synthesis reagents used in the synthesizer are: Detritylated solution is 3% TCA (ABI) in methylene chloride; capping is 16% N-methylimidazole (ABI) and THF in THF In 10% acetic anhydride / 10% 2,6-lutidine (ABI); the oxidizing solution was 16.9 mM I ₂ , 49 mM pyridine, 9% water (PERS) in THF.
EPTIVE (registered trademark). Burdick & Jackson synthetic grade acetonitrile is used directly from the reagent bottle. S-ethyltetrazole solution (0.25 M in acetonitrile) was obtained from American International Chemical, Inc. Create from solids obtained from. Alternatively, a borage reagent (3H-1,2-benzodithiol-3-one 1,1-dioxide, 0.05M in acetonitrile) is used for introduction of phosphorothioate linkages.

RNA deprotection is performed using either a two-pot protocol or a one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on-oligoribonucleotide is transferred to a 4 mL glass screw cap vial and suspended in a solution of 40% aqueous methylamine (1 mL) at 65 ° C. for 10 minutes. After cooling to -20 ° C, the supernatant is removed from the polymer support. The support is washed 3 times with 1.0 mL EtOH: MeCN: H ₂ O / 3: 1: 1, vortexed and then the supernatant is added to the first supernatant. The combined supernatant containing oligoribonucleotides is dried to obtain a white powder. Base deprotected oligoribonucleotides were resuspended in anhydrous TEA / HF / NMP solution (1.5 mL N-methylpyrrolidinone, 750 μL TEA and 1.0 mL TEA · 3HF solution 300 μL, HF concentration 1.4 M) and brought to 65 ° C. Heat. After 1.5 hours, the oligomer is quenched with 1.5M NH ₄ HCO ₃ .

Alternatively, for a one-pot protocol, polymer-bound trityl-on-oligoribonucleotides are transferred to a 4 mL glass screw cap vial and 65% in a solution of 33% ethanolic methylamine / DMSO: 1/1 (0.8 mL). Suspend at 15 ° C. for 15 minutes. Bring the vial to room temperature. TEA • 3HF (0.1 mL) is added and the vial is heated at 65 ° C. for 15 minutes. The sample is cooled to −20 ° C. and then quenched with 1.5M NH ₄ HCO ₃ .

For purification of the trityl-on oligomers, the NH ₄ HCO ₃ solution was stopped, acetonitrile, followed by loading the C-18 containing cartridge that had been prewashed with 50 mM TEAA. After washing the loaded cartridge with water, the RNA is detritylated with 0.5% TFA for 13 minutes. The cartridge is then washed again with water, salt exchanged with 1M NaCl and washed again with water. The oligonucleotide is then eluted with 30% acetonitrile.

  The average step coupling yield is typically> 98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). One skilled in the art will recognize that the scale of synthesis can be larger or smaller than the above example, for example, but not limited to, can be adapted to a 96 well format.

  Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and after synthesis, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al. International Publication WO 93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Nucleosides & Nucleotides, Bio, et al. After protection, they may be joined together by hybridization.

  The siNA molecules of the invention can also be synthesized by a tandem synthesis method as described in Example 1 herein. In this method, both siNA strands are synthesized as a single contiguous oligonucleotide fragment or chain separated by a cleavable linker, which is then cleaved to produce separate siNA fragments or strands. Hybridize to allow purification of the siNA duplex. The linker may be a polynucleotide linker or a non-nucleotide linker. The tandem synthesis of siNA described herein can be readily adapted to any of a multiwell / multiplate synthesis platform, such as a 96 well or similar larger multiwell platform. The tandem synthesis of siNA described herein can also be easily adapted to large scale synthesis platforms using batch reactors, synthesis columns, and the like.

  siNA molecules may also be assembled from two separate nucleic acid strands or fragments, one fragment containing the sense region of the RNA molecule and the second fragment containing the antisense region.

The nucleic acid molecules of the present invention can be extensively modified by modification with nuclease resistant groups such as 2'-amino, 2'-C-allyl, 2'-fluoro, 2'-O-methyl, 2'-H. Stability can be increased (for review, Usman and Cedergren, 1992, TIBS 17, 34; Usman et al., 1994, Nucleic.
Acids Symp. Ser. 31, 163). siNA constructs can be purified by gel electrophoresis using common methods or see high performance liquid chromatography (HPLC; Wincott et al., supra), the entirety of which is hereby incorporated by reference. C) and resuspend in water.

In another aspect of the invention, the siNA molecules of the invention are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vector can be a DNA plasmid or a viral vector. Viral vectors that express siNA can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus or alphavirus. Recombinant vectors capable of expressing siNA molecules can be delivered and left in target cells as described herein. Alternatively, viral vectors that provide transient expression of siNA molecules may be used.

Chemically synthesized nucleic acid molecules having optimized modifications (bases, sugars and / or phosphates) of the nucleic acid molecules of the present invention can prevent degradation by serum ribonucleases, thereby increasing their resistance (Eg, Eckstein et al., International Publication WO 92/07065; Perrart et al., 1990 Nature 344,565; Pieken et al., 1991 Science 253, 314; Usman and
Cedergren, 1992 Trends in Biochem. Sci. 17, 334; Usman et al. , International Publication WO 93/15187; Rossi et al. , International Publication No. WO 91/03162; Sproat, US Pat. No. 5,334,711; Gold et al. , US 6,300,074 and Burgin et al. , (Supra), all of which are hereby incorporated by reference. All of the above references describe various chemical modifications that can be made to the base, phosphate and / or sugar components of the nucleic acid molecules described herein. It is desirable to modify the cell to enhance its drag and to remove bases from the nucleic acid molecule in order to shorten the synthesis time of the oligonucleotide and reduce the need for chemicals.

There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into nucleic acid molecules that can significantly enhance its nuclease stability and efficacy. For example, oligonucleotides are nuclease resistant groups such as 2'-amino, 2'-C-allyl, 2'-fluoro, 2'-O-methyl, 2'-O-allyl, 2'-H, etc. Modified to enhance stability and / or enhance biological activity by modification with base modifications (for review see Usman and Cedergren, 1992 TITBS 17, 34; Usman et al., 1994 Nucleic Acids Symp. Ser. 31, 163; see Burgin et al., 1996 Biochemistry 35, 14090). Sugar modifications of nucleic acid molecules have been widely described in the art (Eckstein et al., International Publication WO 92/07065; Perrart et al. Nature 1990, 344, 565-568; Pieken et al. Science 1991,253, Usman and Cedergren, Trends in Biochem. Sci. 1992, 17, 334-339; Usman et al., International Publication WO 93/15187; Sproat, U.S. Patent No. 5,334,711, Beigelman et al., 1995 J. Am. Biol.Chem.270, 25702; Beigelman et al., International Publication WO97 / 26270; Beigelman et al., US Pat. 24; Usman et al., US Pat. No. 5,627,053; Woolf et al., International Publication WO 98/13526; Thompson et al., US Patent Application 60 / 082,404 (filed April 20, 1998); et al., 1998, Tetrahedron Lett., 39, 1131; 134; and Burlina et al., 1997, Bioorg.Med.Chem., 5, 1999-2010, all of these references are in their entirety. Is hereby incorporated by reference as part of this specification). These publications describe general methods and strategies for determining the position of incorporation of sugar, base and / or phosphate modifications, etc. into nucleic acid molecules without altering the catalytic activity. Quote here as part. In view of such teaching, similar siRNA nucleic acid molecules of the invention may be modified using similar modifications as described herein, unless the ability of siNA to promote RNAi in the cell is significantly inhibited. Can do.

  Although chemical modification of oligonucleotide internucleotide linkages with phosphorothioate, phosphorodithioate, and / or 5'-methylphosphonate linkages improves stability, over-modification can cause some toxicity or reduced activity. Therefore, when designing nucleic acid molecules, the amount of these internucleotide linkages should be minimized. Decreasing the concentration of these bindings should reduce toxicity, increase the potency of these molecules and increase their specificity.

  Short interfering nucleic acid (siNA) molecules having chemical modifications that maintain or enhance activity are provided. Such nucleic acids are also generally more resistant to nucleases than unmodified nucleic acids. Therefore, the activity should not be significantly reduced in vitro and / or in vivo. If regulation is the purpose, the therapeutic nucleic acid molecule delivered externally will optimally remain intracellular until the translation of the target RNA is regulated long enough to reduce the level of unwanted protein. Should be stable. This time varies from hours to days depending on the condition of the disease. Advances in chemical synthesis of RNA and DNA (Wincott et al., 1995, Nucleic Acids Res. 23, 2677; Caruthers et al., 1992, Metals in Enzymology 211, 3-19 (herein incorporated by reference) )), The possibility of altering nucleic acid molecules has been expanded by introducing nucleotide modifications as described above to enhance their nuclease stability.

  In one embodiment, the nucleic acid molecule of the invention comprises one or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) G clamp nucleotides. Including. G-clamp nucleotides are modified cytosine analogs, where the modification confers hydrogen bonding capabilities on both Watson-Crick and Hoogsteen faces of complementary guanines in the duplex. For example, Lin and Matteucci, 1998, J. MoI. Am. Chem. Soc. , 120, 8531-8532. Single G-clamp analog substitutions in the oligonucleotide can substantially enhance helical thermal stability and mismatch discrimination when hybridized to complementary oligonucleotides. By incorporating such nucleotides into the nucleic acid molecules of the present invention, both the affinity and specificity of the nucleic acid target for complementary sequences or template strands are enhanced. In another embodiment, the nucleic acid molecule of the invention has one or more (eg, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) LNA “locked nucleic acids”. Nucleotides such as 2 ′, 4′-C methylene bicyclonucleotides are included (see, eg, Wengel et al., International Publications WO 00/66604 and WO 99/14226).

In another aspect, the invention features conjugates and / or complexes of siNA molecules of the invention. Such conjugates and / or complexes can be used to facilitate delivery of siNA molecules to biological systems such as cells. Conjugates and complexes provided by the present invention treat therapeutic compounds by transporting therapeutic compounds across cell membranes, altering pharmacokinetics, and / or modulating localization of the nucleic acid molecules of the present invention. Activity can be imparted. The present invention includes molecules such as, but not limited to, small molecules, lipids, phospholipids, nucleosides, nucleotides, nucleic acids, antibodies, toxins, negatively charged polymers and other polymers such as proteins, peptides, hormones, carbohydrates, Includes the design and synthesis of new conjugates and complexes for delivering polyethylene glycol, or polyamines, across cell membranes. In general, the transporters described are designed to be used with or without degradable linkers, either individually or as part of a multicomponent system. These compounds are expected to improve the delivery and / or localization of the nucleic acid molecules of the invention to a number of cell types from different tissues in the presence or absence of serum (Sullanger and Cech). , U.S. Pat. No. 5,854,038). The conjugates of the molecules described herein can be attached to a biologically active molecule via a biodegradable linker, such as a biodegradable nucleic acid linker molecule.

  As used herein, the term “biodegradable linker” refers to one molecule to another molecule, eg, a biologically active molecule to a siNA molecule of the invention, or a siNA molecule of the invention. Represents a nucleic acid or non-nucleic acid linker molecule designed as a biodegradable linker for connecting the sense strand and the antisense strand. Biodegradable linkers are designed so that their stability can be modulated for specific purposes, such as delivery to specific tissues or cell types. The stability of nucleic acid based biodegradable linker molecules can be achieved by ribonucleotides, deoxyribonucleotides, and chemically modified nucleotides such as 2′-O-methyl, 2′-fluoro, 2′-amino, 2′-. Adjustments can be made by using various combinations of O-amino, 2'-C-allyl, 2'-O-allyl, and other 2'-modified or base-modified nucleotides. Biodegradable nucleic acid linker molecules can be dimers, trimers, tetramers, or longer nucleic acid molecules, such as about 2,3,4,5,6,7,8,9,10,11,12,13,14,15. , 16, 17, 18, 19, or 20 nucleotides in length, or include a single nucleotide having a phosphate-based linkage, eg, a phosphoramidate or phosphodiester linkage Can do. Biodegradable nucleic acid linker molecules can also include nucleic acid backbones, nucleic acid sugars, or nucleobase modifications.

  As used herein, the term “biodegradable” refers to degradation in a biological system, such as enzymatic degradation or chemical degradation.

  As used herein, the term “biologically active molecule” refers to a compound or molecule capable of eliciting or modulating a biological response in a system. Non-limiting examples of biologically active siNA molecules contemplated by the present invention alone or in combination with other molecules include therapeutically active molecules such as antibodies, hormones, antiviral agents, peptides, proteins , Chemotherapeutic agent, small molecule, vitamin, cofactor, nucleoside, nucleotide, oligonucleotide, enzymatic nucleic acid, antisense nucleic acid, triplex-forming oligonucleotide, 2,5-A chimera, siNA, dsRNA, allozyme, aptamer, decoy And analogs thereof. Biologically active molecules of the present invention include molecules that can modulate the pharmacokinetics and / or pharmacodynamics of other biologically active molecules, such as lipids and polymers, such as polyamines, polyamides Polyethylene glycol and other polyethers are also included.

  As used herein, the term “phospholipid” refers to a hydrophobic molecule that contains at least one phosphate group. For example, the phospholipid can include a phosphate-containing group and a saturated or unsaturated alkyl group, which can be optionally substituted with OH, COOH, oxo, amine, or a substituted or unsubstituted aryl group. .

Externally delivered therapeutic nucleic acid molecules (eg, siNA molecules) are optimally stable in the cell until the reverse transcription of the RNA is regulated long enough to reduce the level of the RNA transcript Should. Nucleic acid molecules are resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of nucleic acid molecules described herein and in the art have the potential to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability, as described above. Enlarged.

  In yet another embodiment, siNA molecules having chemical modifications that maintain or enhance the enzymatic activity of proteins involved in RNAi are provided. Such nucleic acids are also generally more resistant to nucleases than unmodified nucleic acids. Therefore, the activity will not be significantly reduced in vitro and / or in vivo.

  The use of the nucleic acid-based molecules of the present invention will lead to better treatment of disease progression by providing the possibility of combination therapy (eg, multiple siNA molecules targeting different genes, known small molecules). Nucleic acid molecules coupled with molecular inhibitors, or molecules (including different enzymatic nucleic acid molecule motifs) and / or intermittent treatment with a combination of other chemical or biological molecules). Treatment of subjects with siNA molecules also includes combinations of different types of nucleic acid molecules, eg, enzymatic nucleic acid molecules (ribozymes), allozymes, antisense, 2,5-A oligoadenylates, decoys, and aptamers. It is.

  In another aspect, the siNA molecules of the invention have one or more 5 ′ and / or 3′-cap structures, eg, only to the sense siNA strand, only to the antisense siNA strand, or both siNA strands. Including.

  “Cap structure” means a chemical modification incorporated at either end of an oligonucleotide (see, eg, Adamic et al., US Pat. No. 5,998,203 (herein as part of this specification). See quote)). These terminal modifications will protect the nucleic acid molecule from exonucleolytic degradation and help delivery and / or localization in the cell. The cap may be present at the 5 'end (5'-cap), may be present at the 3' end (3'-cap), or may be present at both ends. In a non-limiting example, the 5'-cap is glyceryl, inverted deoxy abasic residue (component); 4 ', 5'-methylene nucleotide; 1- (beta-D-erythrofuranosyl) nucleotide, 4'- Thionucleotide; carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; '-Seconucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3'-3'-inverted nucleotide component; 3'-3'-inverted abasic component; 3'-2 '-Inverted nucleotide component; 3'-2'-inverted abasic component; 1,4-butanediol Acid; is selected from the group consisting of or crosslinked or non-crosslinked methyl phosphonate component; 3'phosphoramidate; Hekishirurin acid; aminohexyl phosphate; 3'-phosphate; 3'phosphorothioate; phosphorodithioate.

In a non-limiting example, the 3′-cap is, for example, glyceryl, inverted deoxy abasic residue (component), 4 ′, 5′-methylene nucleotide; 1- (beta-D-erythrofuranosyl) nucleotide; '-Thionucleotide, carbocyclic nucleotide; 5'-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; Hydroxydecyl phosphate; 1,5-anhydrohexitol nucleotides; L-nucleotides; alpha-nucleotides; modified base nucleotides; phosphorodithioate; threopentofuranosyl nucleotides; 'Seconucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleo 5'-5'-inverted abasic component; 5'-phosphoramidate;5'-phosphorothioate; 1,4-butanediol phosphate; 5'-amino; Selected from the group consisting of cross-linked and / or non-cross-linked 5'-phosphoramidates, phosphorothioates and / or phosphorodithioates, cross-linked or non-cross-linked methylphosphonates and 5'-mercapto components (more particularly Beaucage and Iyer, 1993, Tetrahedron 49, 1925 (herein incorporated by reference).

  The term “non-nucleotide” can be introduced into a nucleic acid strand in place of one or more nucleotide units and includes either sugar and / or phosphate substitutions, with the remaining base being its enzymatic activity. Means any group or compound that is capable of exerting A group or compound is abasic when it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine, and thus lacks a base at the 1 'position.

An “alkyl” group refers to a saturated aliphatic hydrocarbon and includes straight chain, branched chain, and cyclic alkyl groups. Preferably, the alkyl group has 1-12 carbons. More preferably it is a lower alkyl having 1-7 carbons, more preferably 1-4 carbons. Alkyl may or may not be substituted. When substituted, the substituent is preferably hydroxyl, cyano, alkoxy, ═O, ═S, NO ₂ or N (CH ₃ ) ₂ , amino, or SH. The term also includes alkenyl groups that are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight chain, branched chain, and cyclic groups. Preferably, the alkenyl group has 1-12 carbons. More preferably it is a lower alkenyl of 1-7 carbon atoms, more preferably 1-4 carbon atoms. Alkenyl groups may or may not be substituted. When substituted, the substituent is preferably hydroxyl, cyano, alkoxy, ═O, ═S, NO ₂ , halogen, N (CH ₃ ) ₂ ,
Selected from amino or SH. The term “alkyl” also includes alkynyl groups having an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, and includes straight-chain, branched-chain, and cyclic groups. Preferably, the alkynyl group has 1-12 carbons. More preferably it is a lower alkynyl having 1-7 carbons, more preferably 1-4 carbons. Alkynyl groups may or may not be substituted. When substituted, the substituent is preferably hydroxyl, cyano, alkoxy, ═O, ═S, NO ₂ or N (CH ₃ ) ₂ , amino or SH.

Such alkyl groups can also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups. An “aryl” group refers to an aromatic group having at least one ring with a conjugated pi-electron system, and includes carbocyclic aryl, heterocyclic aryl, and diaryl groups. All of these may be optionally substituted. Preferred substituents for the aryl group are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups. An “alkylaryl” group refers to an alkyl group (described above) covalently bonded to an aryl group (described above). A carbocyclic aryl group is a group in which all of the ring atoms of the aromatic ring are carbon atoms. The carbon atom may be optionally substituted. A heterocyclic aryl group is a group having 1-3 heteroatoms as ring atoms in an aromatic ring, with the remainder of the ring atoms being carbon atoms. Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include, for example, furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl, and the like. All of these may be optionally substituted. “Amide” refers to —C (O) —NH—R, wherein R is any of alkyl, aryl, alkylaryl or hydrogen. "
"Ester" represents -C (O) -OR '(wherein R is any of alkyl, aryl, alkylaryl or hydrogen).

As used herein, “nucleotide” is recognized in the art to include natural bases (standard) and modified bases well known in the art. Such bases are generally located at the 1 ′ position of the nucleotide sugar component. Nucleotides generally contain bases, sugars and phosphate groups. Nucleotides may or may not be modified in the sugar, phosphate and / or base components (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides, etc.). For example, Usman and McSwigen (supra); Eckstein et al., International Publication WO 92/07065; Usman et al., International Publication WO 93/15187; To see)). There are several examples of modified nucleobases known in the art, see Limbach et al. , 1994, Nucleic Acids Res. 22, 2183. Some non-limiting examples of base modifications that can be introduced into nucleic acids include, for example, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2,4,6- Trimethoxybenzene, 3-methyluracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidine (eg 5-methylcytidine), 5-alkyluridine (eg ribothymidine), 5-halouridine (eg 5-bromouridine) or 6 -Azapyrimidines or 6-alkylpyrimidines (eg 6-methyluridine), propyne and others (Burgin et al., 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). In this respect, “modified base” means a nucleotide base other than adenine, guanine, cytosine and uracil at the 1 ′ position, or an equivalent thereof.

  In one aspect, the invention features a modified siNA molecule having a phosphate backbone modification, which includes one or more phosphorothioates, phosphorodithioates, methylphosphonates, phosphotriesters, morpholinos, amidates, carbamates. , Carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and / or alkylsilyl substitution. For a review of oligonucleotide backbone modifications, see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, Modern Synthetic Methods, VCH, 331-417, and Mesmaer et al. 1994, Novell Backbone Replacements for Oligonucleotides, Carbohydrate Modifications in Antisense Research, ACS, 24-39.

  “Abasic” means a sugar moiety that lacks a base at the 1 ′ position or has other chemical groups in place of the base (eg, Adamic et al., US Pat. No. 5,998,203). See).

  “Unmodified nucleoside” means any base of adenine, cytosine, guanine, thymine or uracil bonded to the 1 ′ carbon of β-D-ribo-furanose.

  By “modified nucleoside” is meant any nucleotide base that contains a modification in the chemical structure of an unmodified nucleotide base, sugar and / or phosphate. Non-limiting examples of modified nucleotides are shown in Formulas I-VII and / or other modifications described herein.

With respect to the 2′-modified nucleotides described in the present invention, “amino” means 2′-NH ₂ or 2′-O—NH ₂ , which may or may not be modified. Such modifying groups are described, for example, in Eckstein et al. U.S. Pat. No. 5,672,695 and Matric-Adamic et al. U.S. Pat. No. 6,248,878, all of which are hereby incorporated by reference in their entirety.

  Various modifications to the nucleic acid siNA structure can be made to increase the usefulness of these molecules. For example, such modifications increase product life, in vitro half-life, stability, and ease of introducing such oligonucleotides into the target site, eg, increase cell membrane permeability and target cells. Will grant the ability to recognize and combine.

Administration of Nucleic Acid Molecules The siRNA molecules of the present invention can be used alone or in combination with other therapies, for example, HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, and other that can respond to the level of HCV in a cell or tissue. It can be adapted for use in the treatment of indications. For example, siNA molecules can include delivery vehicles such as liposomes, carriers and diluents, and salts thereof for administration to a subject, and / or can be present in a pharmaceutically acceptable formulation. . Methods for delivery of nucleic acid molecules are described in Akhtar et al. , 1992, Trends Cell Bio. , 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995; Maurer et al. 1999, Mol. Membr. Biol. 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol. , 137, 165-192; and Lee et al. . 2000, ACSSymmp. Ser. 752, 184-192, both of which are hereby incorporated by reference. Beigelman et al. , US Pat. No. 6,395,713 and Sullivan
et al. , PCT WO94 / 02595 further describes general methods for delivering nucleic acid molecules. With these protocols, virtually any nucleic acid molecule can be delivered. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art including, but not limited to, encapsulation in liposomes, iontophoresis, or other vehicles such as hydrogels, cyclodextrins (eg, , Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074), biodegradable nanocapsules, and incorporation into bioadhesive spherules, or proteinaceous vectors (O'Hare and Normand, international publication) WO00 / 53722). Alternatively, the nucleic acid / vehicle combination is locally delivered by direct infusion or by using an infusion pump. Direct injection of nucleic acid molecules of the invention can be performed using standard needle and syringe methodologies, or see, for example, Conry et al. 1999, Criva. Cancer Res. 5, 2330-2337 and Barry et al. Can be performed subcutaneously, intramuscularly, or intradermally by the needle-free technique described in International Publication WO99 / 31262. The molecules of the present invention can be used as pharmaceuticals. The medicinal product prevents the disease state in the subject and modulates or treats the onset (all symptoms, preferably all symptoms alleviated).

  That is, the invention features a pharmaceutical composition comprising one or more nucleic acids of the invention in an acceptable carrier, such as a stabilizer, buffer, or the like. The polynucleotide of the present invention can be administered (eg, RNA, DNA or protein) by any standard means by forming a pharmaceutical composition with or without stabilizers, buffers, etc. Can be introduced. If it is desirable to utilize a liposome delivery mechanism, standard protocols for forming liposomes can be followed. The compositions of the present invention are also known as tablets, capsules or elixirs for oral administration; as suppositories for rectal administration; as sterile solutions; as suspensions for infusion administration and as known in the art. It can be formulated and used as another composition that can be used.

  The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the aforementioned compounds, for example, acid addition salts (eg, salts of hydrochloric acid, oxalic acid, acetic acid, and benzenesulfonic acid).

  A pharmaceutical composition or formulation refers to a composition or formulation in a form suitable for administration (eg, systemic administration) to a cell or subject (eg, a human). The appropriate form depends in part on the route of administration used (eg, oral, transdermal, or injection). Such a form should not prevent the composition or formulation from reaching the target cell (ie, the cell to which the negatively charged nucleic acid is desired to be delivered). For example, a pharmaceutical composition that is injected into the bloodstream must be soluble. Other factors are known in the art and include, for example, consideration of toxicity and forms that prevent the composition or formulation from exerting its effect.

  “Systemic administration” means distributed systemically after in vivo systemic absorption or accumulation of the drug in the bloodstream. Routes of administration that provide systemic absorption include, but are not limited to, intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary, and intramuscular. Each of these administration routes exposes siNA molecules of the invention to accessible diseased tissue. The rate at which drugs enter the circulation has been shown to be a function of molecular weight or size. By using liposomes or other drug carriers containing the compounds of the invention, it is possible to localize the drug, for example, to a certain type of tissue (eg, tissue of the reticuloendothelial system (RES)). Liposome formulations that can facilitate the association of the drug with the surface of cells (eg, leukocytes and macrophages) are also useful. This method will enhance the transport of drugs to target cells by exploiting the specificity of immune recognition of abnormal cells (eg, cells producing excess HCV) by macrophages and leukocytes.

“Pharmaceutically acceptable formulation” means a composition or formulation capable of effectively distributing a nucleic acid molecule of the present invention to the physical location most suitable for its desired activity. Non-limiting examples of drugs suitable for formulation with the nucleic acid molecules of the present invention include the following: P-glycoprotein inhibitors (such as Pluronic P85 that can promote drug entry into the CNS) ) (Jolliet-Rient and Tillement, 1999, Fundam. Clin. Pharmacol., 13, 16-26); biodegradable polymers for sustained release transport after intracerebral transplantation, such as poly (DL-lactide-co-glycolide) Microspheres (Emerich, DF et al, 1999, Cell Transplant, 8, 47-58) (Alkermes, Inc. Cambridge, MA); and drugs can be transported across the cerebrovascular barrier, and the mechanism of neural uptake Can be modified, for example polybutylcyanoacrylate Filled nanoparticles are made from bets (Prog Neuropsychopharmacol Biol Psychiatry, 23,941-949,1999). Other non-limiting examples of delivery strategies for nucleic acid molecules of the invention include Boado
et al. 1998, J. MoI. Pharm. Sci. 87, 1308-1315; Tyler et al. 1999, FEBS Lett. , 421, 280-284; Pardridge et al. , 1995, PNAS USA. , 92, 5592-5596; Boado, 1995, Adv. Drug Delivery Rev. , 15, 73-107; Aldrian-Herrada et al. 1998, Nucleic Acids Res. , 26, 4910-4916; and Tyler et
al. 1999, PNAS USA. 96, 7053-7058.

The invention also features the use of a composition comprising surface modified liposomes comprising poly (ethylene glycol) lipids (PEG-modified, or long circulating liposomes or stealth liposomes). These formulations provide a way to increase drug accumulation in the target tissue. This type of drug carrier is resistant to opsonization and elimination by the mononuclear phagocyte system (MPS or RES), thus increasing the blood circulation time of the encapsulated drug and enhancing tissue exposure (Lasic et al. Chem. Rev. 1995, 95,
2601-2627; Ishiwata et al. , Chem. Pharm. Bull. 1995, 43, 1005-1101). Such liposomes have been shown to accumulate selectively in tumors, possibly due to extravasation and capture in angiogenic target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et al. al., 1995, Biochim. Biophys. Acta, 1238, 86-90). Long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, especially compared to conventional cationic liposomes known to accumulate in MPS tissues (Liu et al., J. Biol. Biol.Chem. 1995, 42, 24864-24870; Choi et al., International Publication WO96 / 10391; Ansell et al., International Publication WO96 / 10390; Holland et al., International Publication WO96 / 10392). Long-term circulating liposomes also appear to protect drugs more strongly from nuclease degradation compared to cationic liposomes based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen .

The present invention also includes compositions prepared for storage or administration that include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for use in therapeutic applications are well known in the pharmaceutical art, for example, Remington's Pharmaceutical Sciences, Mack Public.
ishing Co. (AR Gennaro edit. 1985), which is hereby incorporated by reference. For example, preservatives, stabilizers, dyes, and flavoring agents can be used. These include sodium benzoate, sorbic acid, and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents may be used.

  A pharmaceutically effective dose is that dose necessary to prevent, inhibit, or treat a disease state (alleviate symptoms to some extent, preferably alleviate all symptoms). The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical properties of the particular mammal under consideration, the drugs being administered simultaneously, and the pharmaceutical field It depends on other factors that those skilled in the art will recognize. Generally, 0.1 mg / kg-100 mg / kg body weight / day of active ingredient is administered depending on the potency of the negatively charged polymer.

  The nucleic acid molecules of the invention and formulations thereof are administered orally, topically, parenterally, inhaled or in a dosage unit formulation comprising conventional non-toxic pharmaceutically acceptable carriers, adjuvants and vehicles. Can be administered by spray or rectally. As used herein, the term parenteral includes transcutaneous, subcutaneous, intravascular (eg, intravenous), intramuscular, or intrathecal injection or infusion techniques. Further provided is a pharmaceutical formulation comprising a nucleic acid molecule of the present invention and a pharmaceutically acceptable carrier. One or more nucleic acid molecules of the invention are present with one or more non-toxic pharmaceutically acceptable carriers and / or diluents and / or adjuvants and other active ingredients if desired. can do. The pharmaceutical composition containing the nucleic acid molecule of the present invention is in a form suitable for oral use, such as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsions, hard capsules or It can be in the form of a soft capsule or syrup or elixir.

Compositions intended for oral use may be prepared according to any method known in the art for the manufacture of pharmaceutical compositions, and such compositions may be prepared using a pharmaceutically sophisticated mouthpiece. One or more of such sweetening, flavoring, coloring or preserving agents may be included to provide a product that suits. Tablets contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients that are suitable for the manufacture of tablets. These excipients include, for example, inert diluents such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents such as corn starch or alginic acid; binders such as starch , Gelatin or gum arabic, and lubricants such as magnesium stearate, stearic acid or talc. Tablets may be uncoated or may be coated by known techniques. In some cases, such coatings can be prepared by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate can be employed.

  Formulations for oral use include hard gelatin capsules in which the active ingredient is mixed with an inert solid diluent such as calcium carbonate, calcium phosphate or kaolin, or the active ingredient is water or an oily medium such as peanut oil, liquid paraffin Or it may be a soft gelatin capsule mixed with olive oil.

  Aqueous suspensions contain the active materials in admixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum arabic. Dispersants or wetting agents are naturally occurring phosphatides, such as lecithin, or condensation products of alkylene oxides and fatty acids, such as polyoxyethylene stearate, or condensation products of ethylene oxide and long chain fatty alcohols, such as , Heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol, such as polyoxyethylene sorbitol monooleate, or ethylene oxide with partial esters derived from fatty acids and anhydrous hexitol It may also be a condensation product such as polyethylene sorbitan monooleate. Aqueous suspensions also contain one or more preservatives, such as ethyl- or n-propyl-p-hydroxybenzoate, one or more colorants, one or more fragrances, and one or more. It may contain the above sweeteners such as sucrose or saccharin.

  Oily suspensions may be formulated by suspending the active ingredient in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in an inorganic oil such as liquid paraffin. Oily suspensions may contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening and flavoring agents can be added to provide a palatable oral product. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid.

  Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water include the active ingredient in a mixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Give in. Suitable dispersing or wetting agents or suspending agents are as exemplified above. Still other excipients may be present, for example sweetening, flavoring and coloring agents.

  The pharmaceutical composition of the present invention may also be in the form of an oil-in-water emulsion. The oily phase may be a vegetable oil or a mineral oil or mixtures of these. Suitable emulsifiers include naturally occurring gums such as gum arabic or tragagant, naturally occurring phosphatides such as soybeans, lectins, and esters or partial esters derived from fatty acids and hexitol, anhydrides such as sorbitan mono Examples include oleate and condensation products of the partial ester and ethylene oxide, such as polyoxyethylene sorbitan monooleate. The emulsion may contain sweeteners and fragrances.

Syrups and elixirs can be formulated with sweetening agents, for example glycerol, propylene glycol, sorbitol, glucose or sucrose. Such formulations may also contain a demulcent, a preservative and sweetening and coloring agents. The pharmaceutical compositions may be in the form of a sterile injectable aqueous or oleagenous suspension. This suspension may be formulated as known in the art using suitable dispersing or wetting agents and suspending agents described above. A sterile injectable product may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example, a solution in 1,3-butanediol. Also good. Examples of acceptable vehicles and solvents that can be used are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils can be conveniently used as the solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid can be used in the manufacture of injectable medicaments.

  The nucleic acid molecules of the invention can also be administered in the form of suppositories, eg, for rectal administration of the drug. These compositions are made by mixing the drug with a suitable non-irritating excipient that is solid at normal temperature but liquid at rectal temperature and therefore melts in the rectum to release the drug be able to. Such materials include cocoa butter and polyethylene glycol.

  The nucleic acid molecules of the invention can be administered parenterally in a sterile medium. Depending on the vehicle and concentration used, the drug may be suspended or dissolved in the vehicle. It may also be advantageous to dissolve adjuvants such as local anesthetics, preservatives and buffering agents in the vehicle.

  For the treatment of the above mentioned health conditions, dosage levels on the order of about 0.1 mg / kg to about 140 mg / kg body weight per day are useful (about 0.5 mg / day to about 7 g / day per subject). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. Dosage unit forms will generally contain about 1 mg to about 500 mg of an active ingredient.

  The specific dosage level for a particular subject can vary according to factors such as the activity of the specific compound used, age, weight, general health, sex, diet, time of administration, route of administration, and elimination rate, It will be understood that this depends on the combination and the severity of the particular disease being treated.

  For administration to non-human animals, the composition may be added to animal feed or drinking water. It may be convenient to formulate animal feed and drinking water compositions so that the animal can be inoculated with the feed in a therapeutically appropriate amount of the composition. It may also be convenient to produce the composition as a premix for addition to feed or drinking water.

  The nucleic acid molecules of the present invention can also be administered to a subject in combination with other therapeutic compounds to enhance the overall therapeutic effect. The use of multiple compounds in the treatment of an indication can increase the beneficial effects while reducing the presence of side effects.

In one embodiment, the present invention includes a composition suitable for administering a nucleic acid molecule of the present invention to a particular cell type. For example, asialoglycoprotein receptor (ASGPr) (Wu and Wu, 1987, J. Biol. Chem. 262, 4429-4432) is unique to hepatocytes, and branched chain galactose terminal glycoproteins such as asialo-orosomucoid ( ASOR). In another example, the folate receptor is overexpressed in many cancer cells. Binding of such glycoproteins, synthetic glycoconjugates, or folic acid to receptors occurs with an affinity that is strongly dependent on the degree of branching of the oligosaccharide chain. For example, tri antennae structures bind with higher affinity than two antennae or one antenna chain (Baenziger).
and Fiete, 1980, Cell, 22, 611-620; Connolly
et al. , 1982, J. et al. Biol. Chem. 257, 939-945). Lee and Lee (1987, Glycoconjugate J., 4, 317-328) increase this by using N-acetyl-D-galactosamine as the carbohydrate component, which has a higher affinity for the receptor compared to galactose. Specificity was obtained. This “clustering effect” has also been described for the binding and uptake of mannosyl-terminal glycoproteins or glycoconjugates (Ponpipom et al., 1981, J. Med. Client., 24, 1388-1395). Use galactose, galactoseamine, or folic acid-based conjugates to deliver foreign compounds across cell membranes to provide targeted delivery methods for the treatment of, for example, liver disease, liver cancer, or other cancers be able to. The use of bioconjugates can also reduce the required dose of therapeutic compound required for treatment. Furthermore, the bioavailability, pharmacodynamics, and pharmacokinetic parameters of therapeutic agents can be adjusted by using the nucleic acid bioconjugates of the present invention. Non-limiting examples of such bioconjugates are described in Vargeese et al. , U.S. Patent Application No. 10 / 201,394 (filed August 13, 2001); and Matric-Adamic et al, U.S. Patent Application 60 / 362,016 (filed Mar. 6, 2002).

Alternatively, certain siNA molecules of the invention can be expressed in cells from eukaryotic promoters (eg, Izant and Weintraub, 1985 Science 229, 345; McGarry and Lindquist, 1986).
Proc. Natl. Acad. Sci. USA 83, 399; Scanlon et al. 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kasani-Sabet et al. , 1992 Antisense Res. Dev. 2, 3-15; Dropulic et al. 1992
J. et al. Virol 66, 1432-41; Weerasinghe et al. 1991, J. Am. Virol, 65, 5531-4; Ojwang et al. 1992
Proc. Natl. Acad. Sci. USA 89, 10802-6; Chen
et al. , 1992 Nucleic Acids Res. , 20, 4581-9; Sarver et al. , 1990 Science 247, 1222-1225; Thompson et al. 1995 Nucleic Acids Res. 23, 2259; Good et al. 1997, Gene Therapy, 4, 45). One skilled in the art will recognize that any nucleic acid can be expressed from a suitable DNA / RNA vector in a eukaryotic cell. The activity of such nucleic acids can be increased by releasing them from primary transcripts by enzymatic nucleic acids (Draper et al., PCT WO 93/23569, Sullivan et al., PCT WO 94/02595; Ohkawa et al. al., 1992 Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; 55; Chowira et al., 1994 J. Biol. Chem. 269, 25856).

In another aspect of the invention, the RNA molecules of the invention can be expressed from transcription units inserted into DNA or RNA vectors (see, eg, Couture et al., 1996, TIG., 12, 510). ). The recombinant vector may be a DNA plasmid or a viral vector. Viral vectors expressing siNA can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. In another embodiment, polIII based constructs are used to express nucleic acid molecules of the invention (see, eg, Thompson, US Pat. Nos. 5,902,880 and 6,146,886). Recombinant vectors capable of expressing siNA molecules can be delivered as described above and remain in the target cells. Alternatively, viral vectors that give transient expression of nucleic acid molecules can be used. Such vectors can be repeatedly administered as necessary. Once expressed, siNA molecules interact with the target mRNA and produce an RNAi response. Delivery of vectors expressing siNA molecules can be systemic (eg, by intravenous or intramuscular administration), administered to target cells explanted from the patient, and then reintroduced into the subject, or desired target cells. It can be done by any other means that allow introduction into it (for review see Couture et al., 1996, TIG., 12, 510).

In one aspect, the invention features an expression vector that includes a nucleic acid sequence that encodes at least one siNA molecule of the invention. The expression vector can encode one or both strands of the siNA duplex, or a single self-complementary strand that self-hybridizes to produce a siNA duplex. Nucleic acid sequences encoding siNA molecules of the invention can be operably linked in a manner that allows expression of the siNA molecule (eg, Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina
et al. , 2002, Nature Medicine, advance online publication doi: 10.1038 / nm 725).

In another aspect, the invention features an expression vector comprising: a) a transcription initiation region (eg, the initiation region of a eukaryotic pol I, II or III); b) a transcription termination region (eg, a eukaryotic region). A termination region of the organism pol I, II or III); and c) a nucleic acid sequence encoding at least one of the siNA molecules of the invention, said sequence being in a manner allowing the expression and / or delivery of the siNA molecule , Operably connected to the start region and the end region. The vector optionally includes an open reading frame (ORF) of the protein operably linked to the 5 ′ or 3 ′ side of the sequence encoding the siNA of the invention; and / or an intron (intervening sequence). You may go out.

Transcription of siNA molecular sequences can be driven by eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III) promoters. Transcripts from the pol II or pol III promoter are expressed at high levels in all cells. The level of certain pol II promoters in certain types of cells depends on the nature of nearby gene regulatory sequences (enhancers, silencers, etc.). As long as the prokaryotic RNA polymerase enzyme is expressed in suitable cells, a prokaryotic RNA polymerase promoter is also used (Elroy-Stein and Moss, 1990 Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993 Nucleic Acids Res., 21, 2867-72; Lieberet. al., 1993 Methods Enzymol., 217, 47-66; Zhou et al., 1990 Mol. Cell. Biol., 10, 4529-37). Several researchers have shown that nucleic acid molecules expressed from such promoters can function in mammalian cells (eg, Kasani-Sabet et al., 1992 Antisense Res. Dev., 2, 3 -15; Ojwang et al., 1992 Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992 Nucleic Acids R
es. , 20, 4581-9; Yu et al. 1993 Proc. Natl. Acad. Sci. USA, 90, 6340-4; L'Huillier et al.
. , 1992 EMBO J. et al. 11, 4411-8; Lisziewicz et al. 1993 Proc. Natl. Acad. Sci. U. S. A. , 90, 8000-4; Thompson et al. 1995 Nucleic Acids Res. 23, 2259; Sullanger & Cech, 1993, Science, 262, 1566). More particularly, transcription units such as those derived from genes encoding U6 micronuclei (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are highly concentrated in the cell of the desired RNA molecule (eg siNA). (Thompson et al., Supra); Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al. (US Pat. No. 5,1624,803; Good et al., 1997, Gene Ther. 4,45; Beicrelman et al., International Publication WO 96/18736). The siNA transcription unit described above can be incorporated into various vectors for introduction into mammalian cells. Vectors include, but are not limited to, plasmid DNA vectors, viral DNA vectors (eg, adenovirus or adeno-associated virus vectors), or viral RNA vectors (eg, retrovirus or alphavirus vectors) (for review, see Culture and Stinchcomb). , 1996, (supra).

  In another aspect, the invention features an expression vector that includes a nucleic acid sequence encoding at least one of the siNA molecules of the invention in a manner that allows expression of the siNA molecule. In one embodiment, the expression vector comprises a) a transcription initiation region; b) a transcription termination region; and c) a nucleic acid sequence encoding at least one strand of the siNA molecule; the sequence comprises expression of the siNA molecule and / or Alternatively, it is operably connected to the start and end regions in a manner that allows delivery.

In another embodiment, the expression vector comprises a nucleic acid sequence encoding a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; and d) at least one strand of the siNA molecule, Operatively linked to the 3'-end of the open reading frame, the sequence is operable to the start region, open reading frame and stop region in a manner that allows expression and / or delivery of the siNA molecule. So that they are connected. In yet another embodiment, the expression vector comprises a nucleic acid sequence encoding a) a transcription initiation region; b) a transcription termination region; c) an intron; and d) at least one siNA molecule; It is operably linked to the start region, intron and stop region in a manner that allows expression and / or delivery.

In another embodiment, the expression vector comprises a nucleic acid sequence encoding a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; and e) at least one strand of the siNA molecule; This sequence is 3 'of the open reading frame.
-Operably linked to the ends and the sequence is operably linked to the start region, intron, open reading frame and stop region in a manner that allows expression and / or delivery of the siNA molecule. ing.

Biology and biochemistry of HCV In 1989, hepatitis C virus (HCV) was determined to be an RNA virus and identified to be the virus responsible for most non-A non-B hepatitis (Choo et al. , Science. 1989; 244: 359-362). Unlike retroviruses such as HIV, HCV does not pass through the DNA replication phase, and the integrated form of the viral genome in the host chromosome has not been detected (Houghton et al., Hepatology 1991; 14: 381-388). Instead, the replication of the coding (plus) strand is mediated by the generation of the replicating (minus) strand, producing several copies of the plus strand HCV RNA. The genome is composed of a single large open reading frame that is translated into a polyprotein (Kato et al., FEBS Letters. 1991; 280: 325-328). This polyprotein is subsequently subjected to post-translational cleavage resulting in several viral proteins (Leinbach et al., Virology. 1994: 204: 163-169).

Studies of the 9.5 kilobase genome of HCV showed that viral nucleic acids can be mutated at a high rate (Smith et al., Mol. Evol. 1997 45: 238-246). This mutation rate has evolved several distinct genotypes of HCV that share about 70% sequence identity (Simmonds et al., J. Gen. Virol. 1994; 75: 1053-1061). It is important to note that these sequences are very distinct evolutionary. For example, the genetic identity between humans and primates such as chimpanzees is about 98%. Furthermore, HCV infection in a single patient has been shown to be composed of several different and evolved quasispecies with 98% identity at the RNA level. That is, the HCV genome is hypervariable and constantly changing. Although the HCV genome is hypervariable, there are three regions of the genome that are highly conserved. These conserved sequences are present at the 5 'and 3' non-coding regions and at the 5'-end of the core protein coding region and are thought to be essential for HCV RNA replication and HCV polyprotein translation. That is, therapeutic agents that target these conserved HCV genomic regions will have a significant impact on a wide variety of HCV genotypes. Furthermore, drug resistance will not occur with enzymatic nucleic acids specific for conserved regions of the HCV genome. In contrast, therapies that target the inhibition of enzymes such as viral proteases or helicases result in selection of drug-resistant strains because the virally encoded RNAs of these enzymes are located in the hypervariable part of the HCV genome. Will.

After the first exposure to HCV, a transient increase in liver enzymes will occur in the patient. This indicates that an inflammatory process is occurring (Alter et al., IN: Seeff LB, Lewis JH eds. Current Perspectives.
in Hepatology. New York: Plenum Medical Book Co; 1989: 83-89). This increase in liver enzymes will occur at least 4 weeks after the first exposure and will last up to 2 months (Farci et al., New England Journal of Medicine. 1991: 325: 98-104). Prior to elevation of liver enzymes, RT-PCR analysis can be used to detect HCV RNA in patient sera (Takahashi et al., American Journal of Gastroenterology. 1993: 88: 2: 240-243). . This stage of the disease is called the acute stage and usually remains undetected because 75% of patients with acute hepatitis virus from HCV infection are asymptomatic. The remaining 25% of these patients develop jaundice or other symptoms of hepatitis.

Although acute HCV infection is a benign disease, as many as 80% of patients with acute HCV progress to chronic liver disease, which is indicated by a continuous increase in serum alanine aminotransferase (ALT) levels and the continued presence of circulating HCV RNA ( Sherlock, Lancet 1992; 339: 802). Chronic HCV infection progresses spontaneously over 10-20 years, with cirrhosis in 20-50% of patients (Davis et al., Infectious Agents and Disease 1993; 2: 150: 154), leading to HCV-infected hepatocellular carcinoma The progress of is reported in detail (Liang et al., Hepatology. 1993; 18: 1326-1333; Tong et al., Western.
Journal of Medicine, 1994; Vol. 160, no. 2: 133-138). No studies have determined a subpopulation likely to progress to cirrhosis and / or hepatocellular carcinoma. All patients are therefore at equal risk of progression.

  It is important to note that the survival of patients diagnosed with hepatocellular carcinoma is only 0.9-12.8 months from the initial diagnosis (Takahashi et al., American Journal of Gastroenterology. 1993). : 88: 2: 240-243). Treatment with chemotherapeutic agents for hepatocellular carcinoma has proven ineffective and only 10% of patients will benefit from surgery due to the tumor invading a large area of the liver (Trichet) et al., Presse Medicine. 1994: 23: 831-833). Due to the invasive nature of primary hepatocellular carcinoma, the only viable alternative to surgery is liver transplantation (Pichlmayr et al., Hepatology. 1994: 20: 33S-40S).

Patients with chronic HCV infection, when progressing to cirrhosis, develop clinical features common to clinical cirrhosis (D'Amico et al., Digestive Diseases).
and Sciences. 1986; 31: 5: 468-475). These clinical features include hemorrhagic esophageal varices, ascites, jaundice, and brain damage (Zakim D, Boyer TD. Hepatology a textbook of liver.
disease. Second Edition Volume 1.1990 W.M. B. Saunders Company. Philadelphia). In the early stages of cirrhosis, patients are classified as compensated. This means that despite liver tissue injury, the patient's liver can still detoxify metabolites in the bloodstream. In addition, most patients with compensatory liver disease are asymptomatic, and few with symptoms report only minor symptoms such as taste dysfunction and weakness. In later stages of cirrhosis, the patient is classified as decompensated. This means that the patient's ability to detoxify blood metabolites is reduced, and it is at this stage that the clinical features described above appear.

In 1986, D'Amico et al. Described the clinical manifestations and survival rates of 1155 patients with alcohol-related and virus-related cirrhosis (D'Amico, supra).
Of the 1155 patients, 435 (37%) had compensatory disease, but 70% were asymptomatic at the start of the study. The remaining 720 patients (63%) have decompensated liver disease, of which 78% have a history of ascites, 31% have jaundice, 17% have bleeding, and 16% Had brain damage. Hepatocellular carcinoma was found in 6 (0.5%) of patients with compensatory disease and 30 (2.6%) of patients with decompensated disease.

  During the 6-year course, patients with compensatory cirrhosis developed clinical features of decompensated disease at a rate of 10% per year. In most cases, ascites was the first manifestation of decompensation. In addition, at the end of the six-year study, hepatocellular carcinoma developed in 59 patients who initially had compensatory disease.

Regarding survival, the D'Amico study showed that the 5-year survival rate for all patients studied was only 40%. The 6-year survival rate for patients who initially had compensated cirrhosis was 54%, and the 6-year survival rate for patients who initially had decompensated disease was only 21%. There was no significant difference in survival between patients with alcoholic cirrhosis and those with virus-related cirrhosis. The major causes of death in patients in the D'Amico study were liver failure 49%; hepatocellular carcinoma 22%; bleeding 13% (D'A
Mico (above)).

  Chronic hepatitis C is a slowly progressing inflammatory disease of the liver that is mediated by viruses (HCV) and can cause cirrhosis, liver failure and / or hepatocellular carcinoma in 10-20 years. In the United States, it is estimated that 50,000 new cases of acute hepatitis occur each year (NIH Consensus Development Conference on Management of Hepatitis C, March 1997). The prevalence of HCV in the United States is estimated to be 1.8%, and the CDC recognizes that approximately 4.5 million Americans are chronically infected. The CDC also estimates that deaths caused by chronic HCV infection can reach 10,000 people per year.

A number of well-controlled clinical trials using interferon (IFN-alpha) for the treatment of chronic HCV infection have shown about 50% (40% -70%) by the end of 6 months of treatment, with 3 treatments per week. Showed a decrease in serum ALT levels (Davis)
et al. , New England Journal of Medicine 1989; 321: 1501-1506; Marcellin et al. , Hepatology 1991; 13: 393-397; Tong et al. , Hepatology 1997: 26: 747-754; Tong et al. , Hepatology 1997 26 (6): 1640-1645). However, after termination of interferon treatment, approximately 50% of responding patients relapsed, and the ratio of “sustainable” responses was approximately 20-25%, normalized by serum ALT concentration.

HCV RNA can be measured directly using either branched DNA or reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. In general, RT-PCR methods are more sensitive and provide a more accurate assessment of the clinical course (Tong
et al. (Above)). A study that tested 6 months of type 1 interferon therapy using changes in HCV RNA levels as a clinical endpoint showed that 35% of patients lost HCV RNA by the end of treatment (Marceffin et al. (Above)). However, similar to the ALT endpoint, about 50% of patients relapsed 6 months after the end of treatment with only 12% of a sustainable viral response (Marcellin et al, supra). A study that tested 48 weeks of treatment showed that the sustained viral response was 25% or less (NIH Consensus Statement: 1997). Thus, currently the standard for treatment of chronic HCV infection with type 1 interferon is 48 weeks of treatment using changes in HCV RNA concentration as the main assessment of efficacy (Hoofnagle et al., New England Journal of Medicine 1997; 336 (5) 347-356).

Side effects resulting from treatment with type 1 interferon can be divided into four general categories. (1) influenza-like symptoms; (2) neuropsychiatry; (3) laboratory abnormalities; and (4) others (Dusheiko et al., Journal of Viral Hepatitis. 1994: 1: 3-5). Examples of influenza-like symptoms include fatigue, fever; muscle pain; malaise; loss of appetite; tachycardia; chills; Influenza-like symptoms are usually short-lived and tend to relieve after the first 4 weeks of administration (Dushieko et al., Supra). Neuropsychiatric side effects include irritability, indifference; mood changes; insomnia; cognitive changes and depression. The most important of these neuropsychiatric side effects is depression, and patients with a history of depression should not be administered type 1 interferon. Laboratory abnormalities include bone marrow cells such as granulocytes, platelets, and less frequently red blood cells. These blood cell changes rarely lead to significant clinical outcomes (Dushieko et al., Supra). In addition, increased triglyceride levels and elevated serum alanine and aspartate aminotransferase levels have been observed. Finally, thyroid abnormalities have been reported. These thyroid abnormalities are usually reversible after termination of interferon treatment and can be adjusted with appropriate drugs during treatment. Other side effects include nausea; diarrhea; abdominal and back pain; pruritus; hair loss; and rhinorrhea. In general, most side effects will be relieved after 4-8 weeks of treatment (Dushieko et al., Supra).

  Thus, small interfering nucleic acid molecules that target the HCV gene can be used in the treatment and diagnosis of HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, or any other disease or condition that responds to regulation of the HCV gene. A group of novel therapeutic agents is provided.

  The following are non-limiting examples showing the selection, isolation, synthesis and activity of the nucleic acids of the invention.

Example 1: Tandem synthesis of siNA constructs Exemplary siNA molecules of the invention are synthesized in tandem using a cleavable linker, eg, a succinyl-based linker. Following the tandem synthesis described herein, a one-step purification process is performed to obtain RNAi molecules in high yield. This method is very suitable for siNA synthesis supporting high-throughput RNAi screening and can be easily adapted to multi-column or multi-well synthesis platforms.

  After the tandem synthesis (tritylon synthesis) of the siNA oligo and its complementary strand leaving the 5 'terminal dimethoxytrityl (5'-O-DMT) group intact, the oligonucleotide is deprotected as described above. After deprotection, the siNA sequence strand is spontaneously hybridized. This hybridization results in a duplex in which one strand carries a 5'-O-DMT group and the complementary strand contains a terminal 5'-hydroxyl. The newly formed duplex behaves as a single molecule during routine solid phase extraction purification (tritylon purification), even though only one molecule has a dimethoxytrityl group. Since these chains form a stable duplex, this dimethoxytrityl group (or an equivalent group such as another trityl group or other hydrophobic component) can be used to purify an oligo pair using, for example, a C18 cartridge. Only is needed.

Standard phosphoramidite synthesis chemistry is used up to the point of introducing a tandem linker, such as an inverted deoxyabasic succinate or glyceryl succinate linker (see FIG. 1) or equivalent cleavable linker. Non-limiting examples of linker coupling conditions that can be used include interfering bases such as diisopropylethylamine (DIPA) and / or DMAP in the presence of an activator such as bromotripyrrolidinophosphonium hexafluorophosphate (PyBrOP). Is included. After linking the linker, the second sequence is completed using standard synthetic chemistry, leaving the terminal 5'-O-DMT intact. After synthesis, the resulting oligonucleotide is deprotected according to the methods described herein, and the reaction is stopped with an appropriate buffer, such as 50 mM NaOAc or 1.5 M NH ₄ H ₂ CO ₃ .

Purification of siNA duplex can be achieved by solid phase extraction, eg, 1 column volume (CV) acetonitrile, ₂ CV H ₂ O, and ₂ CV 50 mM NaOAc conditioned.
This can be done easily using an rs C18 SepPak lg cartridge. Load the sample and wash with 1 CV H ₂ O or 50 mM NaOAc. Failure array is 1
Elute with CV 14% ACN (aqueous; containing 50 mM NaOAc and 50 mM NaCl). The column is then washed with 1 CV H ₂ O, etc., for example, 1 CV 1% aqueous trifluoroacetic acid (TFA) is passed through the column, then 1 CV 1% aqueous TFA is added to the column and left for about 10 minutes. To detritylize on the column. The remaining TFA solution is removed and the column is washed with H ₂ O, then 1 CV 1M NaCl and again with H ₂ O. The siNA duplex product is then eluted using, for example, 1 CV of 20% aqueous CAN.

  FIG. 2 shows an example of MALDI-TOV mass spectrometry of the purified siNA construct, where each peak corresponds to the calculated mass of the individual siNA strands of the siNA duplex. The same purified siNA gives three peaks when analyzed by capillary gel electrophoresis (CGE). One peak probably corresponds to duplex siNA, and two peaks probably correspond to individual siNA sequence strands. Ion exchange HPLC analysis of the same siNA construct shows only a single peak. Testing of purified siNA constructs using the luciferase reporter assay described below showed that the RNAi activity was the same as compared to siNA constructs generated from separately synthesized oligonucleotide sequence strands.

Example 2: Identification of potential siNA target sites in any RNA sequence The target RNA target, for example the sequence of a viral or human mRNA transcript, is screened for the target site, for example by using a computer folding algorithm. In a non-limiting example, a gene or RNA gene transcript sequence obtained from a database such as Genbank is used to generate a siNA target that is complementary to the target. Such sequences can be obtained from databases or can be determined experimentally as is known in the art. It may be associated with a known target site, for example a target site that has been determined to be an effective target site based on studies with other nucleic acid molecules such as ribozymes or antisense, or a disease or health condition Using known targets, such as sites containing mutations or deletions, siNA molecules targeting these sites can be designed. Various parameters can be used to determine which site is the most appropriate target site in the target RNA sequence. These parameters include, but are not limited to, secondary or tertiary RNA structure, nucleotide base composition of the target sequence, degree of homology between various regions of the target sequence, or relative position of the target sequence in the RNA transcript. It is. Based on these determinations, any number of target sites in the RNA transcript can be selected to screen siNA molecules for efficacy, for example, using in vitro RNA cleavage assays, cultured cells, or animal models. it can. In a non-limiting example, 1-1000 target sites at any position in the transcript are selected based on the size of the siNA construct to be used. High-throughput screening assays for screening siNA molecules can be developed using methods known in the art, such as multi-well or multi-plate assays that determine an effective reduction in target gene expression.

Example 3: Selection of siNA molecule target sites in RNA The following non-limiting steps can be used to select siNAs that target a given gene sequence or transcript.

  1. The target sequence is analyzed in silico to generate a list of all fragments or subsequences of a particular length contained in the target sequence, for example 23 nucleotide fragments. This step is typically performed using a custom Perl script, but commercially available sequence analysis programs such as Oligo, MacVector, or the GCG Wisconsin Package can be used as well.

2. In some cases, siNA corresponds to more than one target sequence. This can occur, for example, when targeting different transcripts of the same gene, targeting different transcripts of two or more genes, or targeting both human genes and animal homologs. In this case, a list of subsequences of a specific length for each target is generated, and then the lists are compared to find a matching sequence in each list. The subsequences are then ranked according to the number of target sequences that contain the given subsequence. The purpose is to find subsequences present in most or all of the target sequences. Alternatively, ranking can identify subsequences that are unique to the target sequence, such as mutant target sequences. Such a method would allow the use of siNAs that specifically target mutant sequences and do not affect the expression of normal sequences.

  3. In some cases, siNA subsequences are not present in one or more sequences, but are present in the desired target sequence. This can occur when siNA targets a gene with a member of the paralogous family that should remain untargeted. As in Case 2 above, generate a list of subsequences of a specific length for each target and then compare the lists to the sequences that are present in the target gene but not in the non-target paralog Find out.

  4). The ranked siNA subsequences can be further analyzed and ranked according to GC content. Sites containing 30-70% GC are preferred, and sites containing 40-60% GC are more preferred.

  5). The ranked siNA subsequences can be further analyzed and ranked according to self-folding and internal hairpins. It is preferred that the internal folding is weaker. Strong hairpin structures should be avoided.

  6). The ranked siNA subsequences can be further analyzed and ranked according to whether they have a sequence of GGG or CCC in the sequence. The presence of GGG (or even more G) on either strand can cause problems in oligonucleotide synthesis and can interfere with RNAi activity. Therefore, this should be avoided as long as better sequences are available. Since CCC places GGG in the antisense strand, it searches in the target strand.

  7). Further analysis of the ranked siNA subsequences results in dinucleotide UU (uridine dinucleotide) at the 3 ′ end of the sequence and / or AA (resulting in 3′UU in the antisense sequence) at the 5 ′ end of the sequence. Rank according to whether or not These sequences make it possible to design siNA molecules with terminal TT thymidine dinucleotides.

  8). Four or five target sites are selected from the list of subsequences ranked as described above. Next, for example, in a subsequence having 23 nucleotides, the right 21 nucleotides of each selected 23-mer subsequence are designed and synthesized for the upper (sense) strand of the siNA duplex, while each selected The reverse complementary strand of the left 21 nucleotides of the 23-mer subsequence is designed and synthesized for the lower (antisense) strand of the siNA duplex (see Tables II and III). If a terminal TT residue is desired for the sequence (as described in paragraph 7), the two 3 'terminal nucleotides on both the sense and antisense strands are replaced with TT before the oligo is synthesized.

  9. siNA molecules are screened in vitro, in cultured cells or in animal model systems to identify the most active siNA molecule, or the most preferred target site in the target RNA sequence.

In another method, a pool of siNA constructs specific for an HCV target sequence is used to express cells expressing HCV RNA, such as human hepatocellular carcinoma (Huh7) cells (eg, Randall et al., 2003, PNAS USA, 100, 235-240) for target sites. The general strategy used in this method is shown in FIG. Non-limiting examples of such pools are SEQ ID NOs: 1-696, 1393-1413, 1417-1419, 1421-1427, 1449-1455, 1477, 1481, 1485, 1487, 1494-1496, 1499, 1501, respectively. -1512, 1549, 1553, 1558-1569, 1582-1593, 1617, 1619, 1621, 1623, and 1625 , 1483, 1489-1491, 1493, 1497-1498, 1500, 1513-1524, 1551, 1556, 1570-1581, 1618, 1620, 1622, 1624, 1626, and 1627 A pool comprising sequences having antisense sequences. Cells expressing HCV (eg, Huh7 cells) are transfected with a pool of siNA constructs to classify cells that exhibit a phenotype associated with HCV inhibition. A pool of siNA constructs can be expressed from a translation cassette inserted in a suitable vector (see, eg, FIGS. 7 and 8). The siNA from cells that show a positive phenotypic change (eg, decreased proliferation, decreased HCV mRNA levels or decreased HCV protein expression) is sequenced to determine the most appropriate target site in the target HCV RNA sequence.

Example 4: siNA design targeting HCV The siNA target site can be generated using the library of siNA molecules described in Example 3 or in vitro siNA system as described in Example 6 herein. Is used to analyze the sequence of HCV RNA targets and optionally prioritize target sites based on folding (the structure of any given sequence analyzed to determine the accessibility of the siNA target) Selected by adding. siNA molecules were designed to be able to bind to their respective targets and optionally individually analyzed by computer folding to assess whether the siNA molecules could interact with the target sequence. Various lengths of siNA molecules can be selected to optimize activity. In general, a sufficient number of complementary nucleotide bases that bind or otherwise interact with the target RNA are selected, but the degree of complementarity to accommodate siNA duplexes of various lengths or base compositions. Can be adjusted. By using such methodologies, siNA molecules can be designed to target any known RNA sequence, eg, a site in the RNA sequence corresponding to any gene transcript.

  Designing chemically modified siNA constructs to preserve the ability to mediate RNAi activity, while maintaining nuclease stability and / or improved pharmacokinetics, localization, and systemic administration in vivo Delivery characteristics can be provided. The chemical modifications described herein are synthetically introduced using the synthetic methods described herein and synthetic methods generally known in the art. The synthetic siNA construct is then assayed for nuclease stability in serum and / or cell / tissue extract (eg, liver extract). Synthetic siNA constructs are also tested in parallel for RNAi activity using a suitable assay, such as the luciferase reporter assay described herein or other suitable assay that can quantify RNAi activity. Synthetic siNA constructs with both nuclease stability and RNAi activity can be further modified and re-evaluated in stability and activity assays. The chemical modification of the stabilized active siNA construct is then applied to any siNA sequence that targets any selected RNA, eg, used in target screening assays, to develop siNA for use in developing therapeutic agents. Compound leads can be picked up (see, eg, FIG. 11).

Example 5: Chemical synthesis and purification of siNA siNA molecules can be designed to interact with various sites in the RNA message, eg, target sequences in the RNA sequences described herein. The sequence of one strand of the siNA molecule is complementary to the target site sequence described above. siNA molecules can be chemically synthesized using the methods described herein. Inactive siNA molecules used as control sequences can be synthesized by scrambling the sequence of the siNA molecule so that it is not complementary to the target sequence. In general, siNA constructs can be synthesized using solid phase oligonucleotide synthesis methods as described herein (eg, Usman et al., US Pat. Nos. 5,804,683; 5,831, 5, 998, 203; 6,117,657; 6,353,098; 6,362,323; 6,437,117; 6,469,158; Scaringe et al., US Pat. No. 6,111,086 ; 6,008,400; 6,111,086 (all of which are hereby incorporated by reference in their entirety).

In a non-limiting example, RNA oligonucleotides are synthesized in a stepwise manner using phosphoramidite chemistry, as is known in the art. In standard phosphoramidite chemistry, 5′-O-dimethoxytrityl, 2′-O-tert-butyldimethylsilyl, 3′-O-2-cyanoethyl N, N-diisopropyl phosphoramidite groups, and exocyclic Nucleosides containing any of the amine protecting groups (eg, N6-benzoyladenosine, N4-acetylcytidine, and N2-isobutyrylguanosine) are used. Alternatively, as described by Scaringe (supra), 2'-O-silyl ethers may be used in combination with acid labile 2'-O-orthoester protecting groups in the synthesis of RNA. Different 2 'chemistries require different protecting groups, for example Usman et
al. Use N-phthaloyl protection for 2′-deoxy-2′-aminonucleosides as described in US Pat. No. 5,631,360, which is hereby incorporated by reference in its entirety. Can do.

  During solid phase synthesis, each nucleotide is added in turn (3'- to 5'-direction) to the solid support-bound oligonucleotide. The first nucleoside at the 3 'end of the chain is covalently attached to a solid support (eg conditioned porous glass or polystyrene) using various linkers. The nucleotide precursor, ribonucleoside phosphoramidite, and activator are mixed to couple the second nucleoside phosphoramidite onto the 5 'end of the first nucleoside. The support is then washed and the unreacted 5'-hydroxyl group is capped using a capping reagent such as acetic anhydride to yield an inactive 5'-acetyl component. Next, the trivalent phosphorus bond is oxidized to form a more stable phosphate bond. At the end of the nucleotide addition cycle, the 5'-O-protecting group is cleaved under suitable conditions (eg, acidic conditions for trityl-based groups and fluoride for silyl-based groups). Repeat this cycle for each next nucleotide.

  Modification of the synthesis conditions, for example, depending on the specific chemical composition of the siNA to be synthesized, different coupling times, different reagent / phosphoramidite concentrations, different contact times, different solid supports and solid support linker chemistries. By using it, the coupling efficiency can be optimized. siNA deprotection and purification can be performed as generally described (Usman et al., US Pat. No. 5,831,071, US Pat. No. 6,353,098, US Pat. No. 6,437,117, Bellon et al., US Pat. No. 6,054,576, US Pat. No. 6,162,909, US Pat. No. 6,303,773 and Scaringe (supra) (all of which are hereby incorporated by reference herein in their entirety). To quote)).

  In addition, the deprotection conditions are modified to obtain the highest yield and purity of siNA construct possible. For example, Applicants have found that oligonucleotides containing 2'-deoxy-2'-fluoro nucleotides can degrade under improper deprotection conditions. Such oligonucleotides are deprotected with aqueous methylamine at about 35 ° C. for 30 minutes. If the 2′-deoxy-2′-fluoro-containing oligonucleotide also contains ribonucleotides, it is deprotected with aqueous methylamine at about 35 ° C. for 30 minutes, then TEA-HF is added, and the reaction is continued for about 15 minutes. Maintain at 65 ° C.

Example 6: RNAi In Vitro Assay for Assessing siNA Activity An siNA construct targeting an HCV RNA target is assessed using an in vitro assay that replicates RNAi in a cell-free system. The assay is described in Tuschl et al. (1999, Genes and Development, 13, 3191-3197) and Zamore et al. (2000, Cell, 101, 25-33) and includes a system adapted for HCV target RNA. RNAi activity is reconstituted in vitro using a Drosophila extract derived from syncytium blastoderm. Target RNA is generated by in vitro transcription using T7 RNA polymerase from an appropriate plasmid expressing HCV, or by chemical synthesis as described herein. Sense and antisense siNA strands (eg, 20 μM each) are added in buffer (eg, 100 mM potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate) at 90 ° C. for 1 minute, then at 37 ° C. for 1 hour. Incubate by incubation and then dilute with lysis buffer (eg 100 mM potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate). Annealing can be monitored by agarose gel gel electrophoresis with TBE buffer and staining with ethidium bromide. Drosophila lysates are prepared using 0-2 hour old embryos from Oregon® flies, collected on yeast molasses agar, and the chorion is removed and lysed. Centrifuge the lysate and isolate the supernatant. The assay comprises a reaction mixture containing 50% lysate [vol / vol], RNA (10-50 pM final concentration), and 10% [vol / vol] lysis buffer containing siNA (10 nM final concentration). . The reaction mixture also contained 10 mM creatine phosphate, 10 μg / ml creatine phosphokinase, 100 μM GTP, 100 μM UTP, 100 μM CTP, 500 μM ATP, 5 mM DTT, 0.1 U / μL RNasin (Promega), And 100 μM of each amino acid. The final concentration of potassium acetate is adjusted to 100 mM. The reaction is pre-assembled on ice and preincubated at 25 ° C. for 10 minutes before adding RNA and incubating at 25 ° C. for an additional 60 minutes. The reaction is stopped with 4 volumes of 1.25 × Passive Lysis Buffer (Promega). Target RNA cleavage is assayed by RT-PCR analysis or other methods known in the art and compared to a control reaction in which siNA is omitted from the reaction.

Alternatively, an internally labeled target RNA for assay is prepared by in vitro transcription in the presence of [alpha- ³² P] CTP, passed through a G50 Sephadex column by spin chromatography and used as the target RNA without further purification. Optionally, target RNA is ^5'32 P-end labeled using T4 polynucleotide kinase enzyme. The assay is performed as described above and the specific RNA cleavage products produced by the target RNA and RNAi are visualized by gel autoradiography. The percent cleavage is determined by quantifying the bands representing the intact control RNA or RNA from the control reaction without siNA and the cleavage product produced by the assay with the PhosphorImager®.

In one embodiment, this assay is used to determine the target site of an HCV RNA target for siNA-mediated RNAi cleavage. That is, multiple siNA constructs for RNAi-mediated cleavage of an HCV RNA target, eg, by analyzing the assay reaction by electrophoresis of labeled target RNA, or by Northern blot, as well as by other methodologies known in the art. Screen.

Example 7 In Vivo Nucleic Acid Inhibition of HCV Target RNA siNA molecules targeting human HCV RNA are designed and synthesized as described above. These nucleic acid molecules can be tested for cleavage activity in vivo, for example by using the following method. The target sequences and nucleotide positions in HCV RNA are shown in Tables II and III.

Two formats are used to test the efficacy of siNA targeting HCV. First, for example, Huh7 cells (eg, Randall et al., 2003, PNAS
USA, 100, 235-240) are used to test reagents in cell culture to determine the extent of RNA and protein inhibition. As described herein, siNA reagents against HCV targets (eg, see Tables II and III) are selected. After these reagents are delivered to, for example, Huh7 cells by an appropriate transfection reagent, RNA inhibition is measured. Real-time PCR monitoring of amplification (eg, ABI 7700 Taqman®) is used to measure the relative amount of target RNA relative to actin. Compare to a mixture of oligonucleotide sequences generated against an irrelevant target or against a randomized siNA control that has the same overall length and chemistry but is randomly substituted at each position. Select and optimize primary and secondary lead reagents for the target. After selecting the optimal transfection reagent concentration, the time course of RNA inhibition is measured using lead siNA molecules.

  Furthermore, RNA inhibition can be determined using a cell-plating format. A non-limiting example of a multi-target screen assaying siNA-mediated inhibition of HCV RNA is shown in FIG. siNA constructs (Table III) were transfected into Huh7 cells at 25 nM, HCV RNA was quantified, and untreated cells ("cell" row in the figure) and lipofectamine transfected cells ("LFA2K" in the figure) Column). As shown in FIG. 18, several siNA constructs show significant inhibition of HCV RNA expression in the Huh7 replicon system. This system is described in Rice et al. (US Pat. Nos. 5,874,565 and 6,127,116, both of which are hereby incorporated by reference).

Delivery of siNA to cells HCV subgenomic replicon clone A or Ava. Huh7b cells stably transfected with 5 are seeded the day before transfection into 96 well plates in DMEM (Gibco), for example 8.5 × 10 ³ cells / well. siNA (final concentration,
For example, 25 nM) and the cationic lipid Lipofectamine 2000 (eg, final concentration 0.5 μl / well) are complexed in Optimem (Gibco) for 20 minutes at 37 ° C. in polypropylene microtubes. After vortexing, complexed siNA is added to each well and incubated for 24-72 hours.

mRNA Taqman Quantitative Total RNA is prepared from cells after siNA delivery, for example, using the Ambion Rnaqueous 4-PCR purification kit for large-scale extractions or the Ambion Rnaqueous-96 purification kit for 96-well assays . For Taqman analysis, for example, a dual labeled probe is synthesized having a reporter dye FAM or VIC covalently attached to the 5 ′ end and a quencher dye TAMARA conjugated to the 3 ′ end. One-step RT-PCR amplification consists of 10 μL total RNA, 100 nM
Forward primer, 100 nM reverse primer, 100 nM probe, 1
XTaqMan PCR reaction buffer (PE-Applied Biosystems), 5.5 mM MgCl ₂ , 100 μM each of dATP, dCTP, dGTP and dTTP,
Using 50 μL of a reaction solution consisting of 0.2 U RNase inhibitor (Promega), 0.025 U AmpliTaq Gold (PE-Applied Biosystems) and 0.2 U M-MLV reverse transcriptase (Promega), for example, ABI PRISM 7700 This can be done with a Sequence detector. Thermal cycling conditions may consist of 40 cycles of 48 ° C. for 30 minutes, 95 ° C. for 10 minutes, then 95 ° C. for 15 seconds and 60 ° C. for 1 minute. Quantification of target mRNA levels is determined against standards made from serially diluted total cellular RNA (300, 100, 30, 10 ng / rxn), eg, 36B4 mRNA of TaqMan reaction, either in parallel or in the same tube Standardize against. For quantification of HCV replicon mRNA, PCR primers and probes specific for the neomycin gene were used:
neo-forward primer, 5'-CCGGCTACCTGCCCATTC-3 '; (SEQ ID NO: 1628)
neo-reverse primer, 5'-CCAGATCATCCCTGATCGACAAG-3 '; (SEQ ID NO: 1629)
neo-probe, 5′FAM-ACATCGCATCGAGCGAGCACGTAC-TAMARA3 ′; (SEQ ID NO: 1630).
For normalization, 36B4 PCR primers and probes were used:
36B4-forward primer, 5'-TCTATCATCAACGGGGTACAAACGA-3 '; (SEQ ID NO: 1631)
36B4 reverse primer, 5'-CTTTTCAGCAGAGTGGGAGAGTG-3 '; (SEQ ID NO: 1632)
36B4 probe, 5 ′ VIC-CCTGGCCTTGTCTGTGGAGACGGATATAMAMA 3 ′; (SEQ ID NO: 1633).

Western blotting nuclear extracts can be prepared using standard micropreparation techniques (see, eg, Andrews and Faller, 1991, Nucleic Acids Research, 19, 2499). For example, a protein extract from the supernatant is prepared using TCA precipitation. An equal volume of 20% TCA is added to the cell supernatant, incubated for 1 hour on ice, and pelleted by centrifugation for 5 minutes. The pellet is washed with acetone, dried and resuspended in water. Cell protein extracts are run on a 10% Bis-Tris NuPage (nuclear extract) or 4-12% Tris-glycine (supernatant extract) polyacrylamide gel and transferred to a nitrocellulose membrane. Non-specific binding can be blocked, for example by incubating with 5% non-fat milk for 1 hour and then reacted with primary antibody at 4 ° C. for 16 hours. After washing, a secondary antibody, eg (1: 10,000 dilution) is applied for 1 hour at room temperature and the signal is detected with SuperSignal reagent (Pierce).

Example 8: A model useful for evaluating downregulation of HCV gene expression
Although there are reports of HCV replication in cell culture cells (see below), these systems are difficult to replicate and are not considered reliable. Therefore, as in the case of the development of other anti-HCV therapies such as interferon and ribavirin, it is possible to proceed directly to clinical utility studies after safety has been demonstrated in animal experiments.

Several recent reports show in vitro growth of HCV in human cell lines (Mizutani et al., Biochem Biophys Res Commun 1996 227 (3): 822-826; Tagawa, et al., Journal of Gastroenterology and. Hepatog
y 1995 10 (5): 523-527; Cribier et al. , Journal of General Virology 76 (10): 2485-2491; Seipp et al. , Journal of General Virology 1997 78 (10) 2467-2478; Iacovacci et al. , Research Virology 1997 148 (2): 147-151; Iocavacci et al. , Hepatology 1997 26 (5) 1328-1337; Ito et al, Journal of General Virology 1996 77 (5): 1043-1054; Nakajima et al. , Journal of Virology 1996 70 (5): 3325-3329; Mizutani et al. , Journal of Virology 1996 70 (10): 7219-7223; Valli et al. , Res Virol 1995 146 (4): 285-288; Kato et al. , Biochem Biophys Res Comm. 1995 206 (3): 863-869). HCV replication has been shown in both T and B cell lines, as well as in cell lines derived from human hepatocytes. Replication was demonstrated using either an RT-PCR based assay or a b-DNA assay. It is important to note that the most recent publications on HCV cell culture have demonstrated replication up to 6 months. However, the level of HCV replication observed in these cell lines is not high enough to screen for antiviral compounds.

  In addition to cell lines that can be infected with HCV, several groups have reported successful transformation of cell lines with full-length or partial HCV genomic cDNA clones (Harada et al., Journal). of General Virology 1995 76 (5) 1215-1221; Haramatsu et al., Journal of Viral Hepatitis 1997 4S (1): 61-67; Dash et al, American Journal 3 19 ol. et al., Gasterenterology 1995 109 (6): 1933-40; Yoo et al., Jour. al Of Virology 1995 69 (1): 32-38).

  The recent development of a subgenomic HCV RNA replicon that has been successfully replicated in Huh7, a human hepatocellular carcinoma cell line, represents a significant advance towards a reliable cell culture model. These replicons contain a neomycin gene upstream of the HCV nonstructural gene and allow selection of RNA that can replicate in Huh7 cells. Initially, RNA replication was detected at a low frequency (Lohmann et al. Science 1999 285: 110-113), but the identification of replicons with cell-adaptive mutations in the NS5A region resulted in a replication efficiency of 10 , 000-fold (Blight et al. Science 2000 290: 972-1975). HCV life cycle steps such as translation, protein processing, and RNA replication are reproduced in the subgenomic replicon system, but no early events (virus attachment and uncoating) and virus assembly occur. Incorporation of the structural gene of HCV into the replicon produces HCV core and envelope proteins but does not result in viral assembly (Pietschmann et al. Journal of Virology 2002 76: 4008-4021). Using such a replicon system, siRNA-mediated HCV RNA inhibition has been studied (see, for example, Randall et al., 2003, PNAS USA, 100, 235-240).

In some cell culture systems, cationic lipids have been shown to enhance the bioavailability of oligonucleotides to cultured cells (Bennet, et al., 199).
2, Mol. Pharmacology, 41, 1023-1033). In one embodiment, the siNA molecules of the invention are complexed with a cationic lipid for cell culture experiments. The siNA and cationic lipid mixture is prepared in serum free DMEM just prior to addition to the cells. The DMEM plus additive is warmed to room temperature (about 20-25 ° C.), the cationic lipid is added at the desired final concentration, and the solution is vortexed lightly. The siNA molecule is added to the desired final concentration and the solution is vortexed again and incubated for 10 minutes at room temperature. In dose response experiments, the RNA / lipid complex is serially diluted with DMEM after 10 minutes of incubation.

Animal models Assessing the efficacy of anti-HCV agents in animal models is an important prerequisite for human clinical trials. The best-characterized animal system for HCV infection is chimpanzee. Furthermore, chronic hepatitis caused by HCV infection in chimpanzees and humans is very similar. Although clinically relevant, the chimpanzee model has several practical obstacles and is difficult to use. For example, the cost is high, long incubation is required, and a sufficient amount of animals cannot be obtained. Because of these causes, many groups have attempted to develop a rodent model of chronic hepatitis C infection. Although direct infection is not possible, several groups have reported stable transfection of some or all of the HCV genome into rodents (Yamamoto et al.
al. Hepatology 1995, 22 (3): 847-855; Galun.
et al. , Journal of Infectious Disease 1995 172 (1): 25-30; Koike et al. , Journal of General Virology 1995 76 (12) 3031-3038; Pasquinelli et al. Hepatology 1997 25 (3): 719-727; Hayashi et al. , Prince Takamatsu
Symp 1995 25: 143-149; Maria et al. , Journal of General Virology 1997 78 (7) 1527-1531; Takehara et al. Hepatology 1995 21 (3): 746-751; Kawamura et al. , Hepatology 1997 25 (4): 1014-1021). Furthermore, when HCV-infected human liver is transplanted into immunocompromised mice, HCV RNA is detected longer in the blood of the animal.

  A method for expressing hepatitis C virus in an in vivo animal model has been developed (Vierling, International Publication WO99 / 16307). Viable HCV-infected human hepatocytes are transplanted into the liver parenchyma of scid / scid mouse hosts. The scid / scid mouse host is then maintained in a viable state so that viable, morphologically intact human hepatocytes remain in the donor tissue and hepatitis C virus remains Duplicate in. This model provides an effective means to study HCV inhibition by enzymatic nucleic acids in vivo.

Example 9: RNAi-mediated inhibition of HCV RNA expression siNA constructs (eg, siNA constructs shown in Table III) are tested for efficacy in reducing HCV RNA expression, eg, in Huh7 cells (see, eg, Randall et al. , 2003, PNAS USA, 100, 235-240). Cells are seeded in 96-well plates at 5,000-7,500 cells / well, 100 μl / well approximately 24 hours prior to transfection so that the cells are 70-90% confluent at the time of transfection. For transfection, annealed siNA is mixed with transfection reagent (Lipofectamine 2000, Invitrogen) in a volume of 50 μl / well and incubated for 20 minutes at room temperature. The siNA transfection mixture is added to the cells to a final siNA concentration of 25 nM in a volume of 150 μl. Each siNA transfection mixture is added to 3 wells for 3 siNA treatments. Cells are incubated for 24 hours at 37 ° C. in the continuous presence of siNA transfection mixture. At 24 hours, RNA is prepared from each well of treated cells. First, the supernatant with the transfection mixture is removed and discarded, then the cells are lysed and RNA is prepared from each well. Target gene expression after treatment is assessed by RT-PCR for the target gene and control gene (36B4, RNA polymerase subunit) for normalization. Average the data from three experiments and determine the standard deviation for each treatment. Normalized data is presented graphically and the percent reduction of target mRNA by active siNA is determined relative to the respective inversion control siNA.

  Non-limiting examples include siNA constructs containing ribonucleotides and a 3 ′ terminal dithymidine cap, and 2′-deoxy-2′-fluoropyrimidine nucleotides and purine ribonucleotides, where the sense strand of siNA is 5 ′ and 3 A chemically modified siNA construct is assayed that is further modified with a 'terminal inverted deoxyabasic cap and the antisense strand contains a 3' terminal phosphorothioate internucleotide linkage. Activity is similarly assayed for additional stabilizing chemistries described in Table IV. These siNA constructs are compared to the appropriate matched chemistry reversal control. In addition, siNA constructs are also compared to untreated cells, cells transfected with lipids and scrambled siNA constructs, and cells transfected with lipids only (transfection control).

Example 10: ChiNA HCV / Poliovirus siNA Inhibition in HeLa Cells Inhibition of chimeric HCV / poliovirus was investigated in HeLa cells using a 21 nucleotide siNA duplex. Seven siNAs were designed that target three regions in the highly conserved 5 ′ untranslated region (UTR) of HCV RNA. SiNA was screened in two cell culture systems that depend on the 5'-UTR of HCV. One requires translation of the HCV / luciferase gene and the other requires replication of the chimeric HCV / poliovirus (PV) (Blatt et al., US patent application 09 / 740,332 (December 18, 2000). See Japanese application, cited herein as part of this specification). Transfection of the HCV / PV system was performed on HeLa cells (grown in DMEM supplemented with sodium pyruvate and 100 mM HEPES and 5% FBS) with either 10 nM or 25 nM of the cationic lipid NC168 or LFA2K. Performed at siNA concentration. HeLa cells were inoculated with HCV / PV virus at moi = 0.01 pfu / cell for 30 minutes in serum-free medium. The inoculum was removed, 80 μL of medium was added, and 20 μL of transfection complex was added to each well. Cells and supernatants were frozen 20-24 hours after transfection. Each plate was processed in 3 freeze-thaw cycles and the supernatant was collected. The supernatant was applied to HeLa cells for 3 days, then stained and counted. The results shown in FIGS. 14-17 are expressed as pfu / ml × 10 ⁵ .

Two siNAs (29579/29586 and 29578/2958) targeting the same region (1 nucleotide shift) are active in both systems (see FIG. 12). For example, in cells treated with siNA, more than 85% reduction in HCVPV replication was observed compared to the inverted siNA control 29593/29600 (FIG. 12), and the IC50 was about 2.5 nM (FIG. 13). In order to develop nuclease resistant siNA for in vivo applications, siNA can be modified to include stabilizing chemical modifications. Such modifications include phosphorothioate linkages (P = S), 2′-O-methyl nucleotides, 2′-fluoro (F) nucleotides, 2′-deoxy nucleotides, universal base nucleotides in one or both of the siNA strands, 5 'and / or 3' terminal modifications and various other nucleotide and non-nucleotide modifications, such as those described herein, are included. By using this systematic approach, active siNA molecules were identified that were substantially more resistant to nucleases. Some of these constructs are HC
Tested with the V / poliovirus chimera system showed a significant reduction in viral replication (see FIGS. 14-17). The siNA constructs shown in FIGS. 14-17 are indicated by cross-referenced RPI numbers in Table III. siNA activity is compared to the appropriate control (untreated cells, scrambled / inactive control sequences, or transfection controls). FIG. 14 shows inhibition of HCV RNA using chemically modified siNA construct 30051/30053 in the HCV / poliovirus chimera system. This construct has inverted deoxyabasic nucleotides, several phosphorothioate linkages, and 5-nitroindole nucleotides at the 3 'and 5' ends. FIG. 15 shows inhibition of HCV RNA using chemically modified siNA construct 30055/30057 in the HCV / poliovirus chimera system. This construct has inverted deoxyabasic nucleotides, several phosphorothioate linkages, and 5-nitroindole nucleotides at the 3 'and 5' ends. FIGS. 16 and 17 show unmodified siNA constructs (29586/29579) and chemically modified siNA constructs (30417/30419, 30417/30420, 30418/30419, and combinations thereof) at 10 nM and 25 nM, respectively. FIG. 5 shows inhibition of HCV RNA in the HCV / poliovirus chimera system used in siNA. As shown in FIGS. 14-17, the siNA constructs of the present invention provide potent inhibition of HCV RNA in the HCV / poliovirus chimeric system. Thus, siNA constructs, such as chemically modified, nuclease resistant siNA molecules, are important therapeutic agents for treating chronic HCV infection.

Example 11: Current knowledge in indications HCV research demonstrates the need for methods to assay HCV activity and compounds that can regulate HCV expression for research, diagnostic and therapeutic uses. As described herein, the nucleic acid molecules of the invention can be used in assays to diagnose disease states associated with HCV levels. In addition, nucleic acid molecules can be used to treat disease states associated with HCV levels.

  Specific degenerative and disease states that may be associated with modulation of HCV expression include, but are not limited to, HCV infection, liver failure, hepatocellular carcinoma, cirrhosis, and / or other disease states associated with HCV infection.

Example 12: Interferon Interferon is a non-limiting example of a group of compounds that can be used in combination with the siNA molecules of the invention to treat the diseases and / or conditions described herein. Type I interferon (IFN) is a group of natural cytokines that includes more than 25 IFN-α families (Pesta, 1986, Methods Enzymol. 119, 3-14), and IFN-β and IFN-ω. is there. Although they are evolutionarily derived from the same gene (Diaz et al., 1994, Genomics 22, 540-552), there are many differences in the primary sequence of these molecules, and biological activity is evolutionary. It is implied that it has branched off. All type I IFNs share a common pattern of biological effects that begins with IFN binding to cell surface receptors (Pfeffer & Strulovici, 1992, Transmembrane brand messengers for IFN-α / β.In: Interferon.Principles. and Medical Applications., S. Baron, DH Coopenhaver, F. Dianzani, WR Fleischmann Jr., TK Hughes Jr., GR Kimpel, D. W. Nisel, G. J. Stanton, and SK Tyring, eds. 151-160). After binding, tyrosine kinases such as Janus tyrosine kinase and STAT protein are activated to produce several IFN-stimulated gene products (Johnson et al., 1994, Sci. Am. 270, 68). -75). IFN-stimulatory gene products are responsible for the multifaceted biological effects of type I IFN, including antiviral, antiproliferative and immunomodulatory effects, cytokine induction, and HLA class I and class II regulation (Pestka et al. al., 1987, Annu. Rev. Biochem 56, 727). Examples of IFN-stimulating gene products include 2-5-oligoadenylate synthase (2-5 OAS), β2-microglobulin, neopterin, p68 kinase, and Mx protein (Chebath & Revel, 1992, The 2-5 A system: 2-5 A synthetase, isospecies and functions.In: Interferon.Principles and Medical Applications.S.Baron, D.H. Copenhaver, F. DianT. G. R. Kimpel, D. W. Niesel, G. J. Stanton, and S. K. Tyring, eds., Pp. 225-23 Samuel, 1992, The RNA-dependent P1 / eIF-2α protein kinase.In: Interferon.Principles and Medical Applications.S.Baron, D.H. Coanhaver, F. DianR. F. DianR. K. Hughes Jr., G. R. Kimpel, D. W. Niesel, G. H. Stanton, and S. K. Tyring, eds. 237-250; Horisberger, 1992, MX protein: function and Mechanism. In: Interferon.Principles and Medical Application ns S Baron, DH Coopenhaver, F. Dianzani, WR Freischmann Jr., TK Hughes Jr., GR Kimpel, DK Niesel, GH Stanton, and SK Tyring, eds. 215-224). All type I IFNs have similar biological effects, but not all activities are common to each type I IFN, and in many cases the degree of activity varies greatly with each IFN subtype ( Fish et al, 1989, J. Interferon Res. 9, 97-114; Ozes et al., 1992, J. Interferon Res. 12, 55-59). More specifically, studies of the properties of different subtypes of IFN-α and molecular hybrids of IFN-α showed differences in pharmacological properties (Rubinstein, 1987, J. Interferon Res. 7, 545-551). . These pharmacological differences can also be caused by changes of about 3 amino acid residues (Lee).
et al. , 1982, Cancer Res. 42, 1312-1316).

  85-166 amino acids are conserved in known IFN-α subtypes. Except for the IFN-α pseudogene, about 25 different IFN-α subtypes are known. Comparison of these non-allelic subtype pairs showed that the primary sequence difference was 2% -23%. In addition to naturally occurring IFN, non-natural recombinant type I interferon known as consensus interferon (CIFN) was synthesized as a therapeutic compound (Tong et al., 1997, Hepatology 26, 747-754).

Interferons are currently used in at least 12 different indications, including infectious and autoimmune diseases and cancer (Borden, 1992, N. Engl. J. Med. 326, 1491-1492). For autoimmune diseases, IFN has been used to treat rheumatoid arthritis, multiple sclerosis and Crohn's disease. For the treatment of cancer, IFN has been used alone or in combination with many different compounds. Specific types of cancer for which IFN is used include squamous cell carcinoma, melanoma, adrenal gland, hemangioma, ciliary cell leukemia and Kaposi's sarcoma. In the treatment of infectious diseases, IFN increases phagocytic activity of macrophages and leukocyte cytotoxicity and inhibits the growth of cellular pathogens. Specific indications for which IFN has been used for treatment include hepatitis B, human papillomavirus types 6 and 11 (ie, genital warts) (Leventhal et al.)
al. 1991, N.M. Engl. J. et al. Med. 325, 613-617), chronic granulomatous disease and hepatitis C virus.

  A number of well-controlled clinical trials of IFN-alpha in the treatment of chronic HCV infection have shown that approximately 50% of patients (range 40% -70%) at the end of 6 months of treatment, with 3 treatments per week (Davis et al., 1989, The New England Journal of Medicine 321, 1501-1506; Marcellin et al., 1991, Hepatology 13, 393-397; Tong et al. 1997, Hepatology 26, 747-754; Tong et al., Hepatology 26, 1640-1645). However, after discontinuing interferon treatment, approximately 50% of responding patients relapsed and the “permanent” response rate was approximately 20-25% as assessed by normalization of serum ALT concentrations. In addition, studies that tested 6 months of type I interferon treatment using changes in HCV RNA values as clinical endpoints showed that up to 35% of patients lost HCV RNA by the end of treatment ( Tong et al., 1997, supra). However, with regard to the ALT endpoint, approximately 50% of patients relapsed 6 months after discontinuation of treatment, with only 12% (23) of permanent viral responses. Studies that tested 48 weeks of treatment showed that the sustained viral response was up to 25%.

Pegylated interferon, ie, interferon conjugated with polyethylene glycol (PEG), exhibits improved properties over interferon. Benefits afforded by PEG conjugation include an improved pharmacokinetic profile compared to interferon without PEG, and thus a more convenient dosing regimen, improved tolerance, and improved antiviral Efficacy is given. Such improvements include polyethylene glycol interferon alpha-2a (PEGASYS, Roche) and polyethylene glycol interferon alpha-2b (VIRAFERON).
PEG, PEG-INTRON, Enzon / Schering Plow).

  SiNA molecules in combination with interferon and polyethylene glycol interferon have the potential to improve the efficacy of treatment of HCV or any of the other indications mentioned above. Enhanced efficacy can be achieved using siNA molecules that target RNA associated with diseases such as HCV infection, either individually or in combination with other therapies such as interferon and polyethylene glycol interferon.

Example 13: Diagnostic Applications The siNA molecules of the present invention can be used in various applications, eg, in clinical, industrial, environmental, agricultural and / or research settings, for various diagnostic applications, such as identification of molecular targets (eg RNA). Can be used. Use in the diagnosis of such siNA molecules includes utilizing reconstituted RNAi systems, such as cell lysates or partially purified cell lysates. The siNA molecule of the present invention can be used as a diagnostic tool to examine genetic drift and mutations in diseased cells or to detect the presence of endogenous or foreign (eg, viral) RNA in cells it can. Due to the close relationship between siNA activity and target RNA structure, mutations that alter base pairing and three-dimensional structure of the target RNA can be detected in any region of the molecule. By using multiple siNA molecules described in the present invention, nucleotide changes important for RNA structure and function in vitro and in cells and tissues can be mapped. Cleavage of target RNA by siNA molecules can be used to inhibit gene expression and reveal the role of specific gene products in the progression of disease or infection. In this way, other gene targets can be identified as important mediators of the disease. These experiments will lead to better treatment of disease progression by providing the possibility of combination therapy (eg, combined with multiple siNA molecules targeting different genes, known small molecule inhibitors) intermittent treatment in combination with siNA molecules, siNA molecules and / or other chemical or biological molecules). Other in vitro uses of the siNA molecules of the invention are well known in the art and include the detection of the presence of mRNA associated with a disease, infection or associated health condition. Such RNA is detected after treatment with siNA molecules by determining the presence of cleavage products using standard methodologies such as fluorescence resonance energy transfer (FRET).

  In a specific example, siNA molecules that can only cleave only wild-type or mutant forms of the target RNA are used in the assay. The first siNA molecule (ie, that cleaves only wild type target RNA) is used to identify the presence of wild type RNA in the sample, and the second siNA molecule (ie, cleave only mutant type target RNA) To identify the mutant RNA in the sample. As a reaction control, the synthetic substrate of both wild-type and mutant RNA is cleaved with both siNA molecules, revealing the relative efficiency of the siNA molecule in the reaction and not cleaving the “non-target” RNA species. The cleavage products from the synthetic substrate also serve to generate size markers for the analysis of wild type and mutant RNA in the sample population. Thus, each analysis requires two siNA molecules, two substrates, and one unknown sample, which are combined to perform six reactions. The presence of the cleavage product is confirmed using an RNase protection assay so that the full length and cleavage fragment of each RNA can be analyzed in one lane of a polyacrylamide gel. The results need not necessarily be quantified in order to gain insight into the expression of the mutant RNA in the target cell and the estimated risk of the desired phenotypic change. Expression of mRNA, where the protein product is suggested to be involved in the development of a phenotype (ie, associated with disease or associated with infection) is sufficient to establish risk. If equivalent specific activity probes are used for both transcripts, a qualitative comparison of RNA levels is sufficient and the cost of initial diagnosis is reduced. Whether comparing RNA levels qualitatively or quantitatively, a higher mutant to wild type ratio will correlate with higher risk.

  All patents and publications mentioned in this specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All references cited in this specification are cited as part of this specification to the same extent as if each reference was individually cited herein in its entirety as part of this specification. The

  Those skilled in the art will readily appreciate that the present invention is well adapted to carry out its objectives and obtain the results and advantages described, as well as those inherent herein. The methods and compositions described herein are representative of presently preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Those skilled in the art will make modifications and other uses that fall within the spirit of the invention as defined in the claims.

Those skilled in the art will readily appreciate that various substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. That is, such additional aspects are within the scope of the present invention and claims. The present invention teaches those skilled in the art to test various combinations and / or substitutions of the chemical modifications described herein to obtain nucleic acid constructs with improved activity that mediate RNAi activity. Such improved activity can include improved stability, improved bioavailability, and / or improved activation of cellular responses that mediate RNAi. Thus, the specific embodiments described herein are not limiting and one of ordinary skill in the art will be able to identify the siNA molecules with improved RNAi activity without modification of the modifications described herein without undue experimentation. It can be readily understood that certain combinations can be tested.

The invention described herein as an example can be practiced appropriately without any elements or limitations not specifically disclosed herein. That is, for example, in each example in this specification, the terms “including”, “consisting essentially of ...” and “consisting of ...” are replaced with either of the other two. be able to. The terms and expressions used in this specification are used as terms of description and are not limiting. The use of such terms and expressions is not intended to exclude the features shown and described, or equivalents thereof, but is within the scope of the invention as set forth in the claims. It will be understood that various modifications are possible. That is, although the invention has been specifically disclosed by preferred embodiments and optional features, those skilled in the art can make changes and variations in the concepts described herein, and such changes and variants are also claimed. It should be understood that it is considered to be within the scope of the present invention as defined in

  Furthermore, if the features and aspects of the invention are described in terms of Markush groups or other alternative groups, those skilled in the art will also describe the invention in terms of individual members or subgroups of Markush groups or other groups. You will recognize that.

Claims (35)

A double-stranded short interfering nucleic acid (siNA) molecule that inhibits hepatitis C virus (HCV) replication, wherein one strand of the double-stranded siNA molecule is complementary to the nucleotide sequence of HCV RNA or a part thereof. An antisense strand comprising a nucleotide sequence, the other strand is a sense strand comprising a nucleotide sequence complementary to the nucleotide sequence of the antisense strand, and most of the pyrimidine nucleotides present in said double stranded siNA molecule are sugar SiNA molecules characterized in that they contain modifications. 2. The siNA molecule of claim 1, wherein the HCV RNA comprises HCV negative strand RNA. The siNA molecule of claim 1, wherein the HCV RNA comprises HCV plus strand RNA. The siNA molecule of claim 1, wherein the siNA molecule does not comprise ribonucleotides. The siNA molecule of claim 1, wherein the siNA molecule comprises a ribonucleotide. 2. The siNA molecule of claim 1, wherein all pyrimidine nucleotides in the siNA molecule comprise a sugar modification. Modified pyrimidine nucleotides are 2′-deoxy-pyrimidine, 2′-O-alkylpyrimidine, 2′-C-alkylpyrimidine, 2′-deoxy-2′-fluoro-pyrimidine, 2′-aminopyrimidine, 2 ′. 7. The siNA molecule of claim 6, selected from -methoxy-ethoxypyrimidine, and 2'-O, 4'-C-methylenepyrimidine nucleotides alone or in any combination. 8. The siNA molecule of claim 7, wherein the 2'-O-alkylpyrimidine nucleotide is 2'-O-methyl or 2'-O-allyl. The siNA molecule according to claim 1, wherein the nucleotide sequence of the antisense strand of the double-stranded siNA molecule is complementary to RNA encoding the HCV protein or fragment thereof. 2. The siNA molecule of claim 1, wherein each strand of the siNA molecule comprises about 19 to about 29 nucleotides, each strand comprising at least about 19 nucleotides complementary to the nucleotides of the other strand. 2. The siNA molecule is assembled from two oligonucleotide fragments, one fragment comprising the nucleotide sequence of the antisense strand of the siNA molecule and the second fragment comprising the nucleotide sequence of the sense strand of the siNA molecule. siNA molecule. The siNA molecule of claim 1, wherein the sense strand is linked to the antisense strand via a linker molecule. The siNA molecule of claim 12, wherein the linker molecule is a polynucleotide linker. The siNA molecule of claim 12, wherein the linker molecule is a non-nucleotide linker. The siNA molecule of claim 1, wherein any pyrimidine nucleotide present in the sense strand is a 2'-deoxy-2'-fluoropyrimidine nucleotide and any purine nucleotide present in the sense region is a 2'-deoxypurine nucleotide. . The siNA molecule of claim 1, wherein the sense strand comprises a 3 'end and a 5' end, and wherein there is an end cap component at the 5 'end, 3' end, or both the 5 'end and the 3' end of the sense strand. . 17. The siNA molecule of claim 16, wherein the end cap component is an inverted deoxy abasic component. The siNA molecule of claim 1, wherein the antisense strand comprises one or more 2'-deoxy-2'-fluoropyrimidine nucleotides and one or more 2'-O-methylpurine nucleotides. 2. Any pyrimidine nucleotide present in the antisense strand is a 2′-deoxy-2′-fluoropyrimidine nucleotide and any purine nucleotide present in the antisense strand is a 2′-O-methyl purine nucleotide. The described siNA molecule. The siNA molecule of claim 1, wherein the antisense strand comprises a phosphorothioate internucleotide linkage at the 3 'end of the antisense strand. The siNA molecule of claim 1, wherein the antisense strand comprises a glyceryl modification at the 3 'end of the antisense strand. The siNA molecule of claim 1, wherein each strand of the siNA molecule comprises 21 nucleotides. About 19 nucleotides of each strand of the siNA molecule base pair with complementary nucleotides of the other strand of the siNA molecule, and at least two 3 'terminal nucleotides of each strand of the siNA molecule are nucleotides and bases of the other strand of the siNA molecule 23. The siNA molecule of claim 22, which does not pair. 24. The siNA molecule of claim 23, wherein the two 3 'terminal nucleotides of each fragment of the siNA molecule is 2'-deoxy-pyrimidine. 25. The siNA molecule of claim 24, wherein the 2'-deoxy-pyrimidine is 2'-deoxy-thymidine. 23. The siNA molecule of claim 22, wherein 21 nucleotides of each strand of the siNA molecule base pair with a complementary nucleotide of the other strand of the siNA molecule. 23. The siNA molecule of claim 22, wherein about 19 nucleotides of the antisense strand base pair with the nucleotide sequence of HCV RNA or a portion thereof. 23. The siNA molecule of claim 22, wherein 21 nucleotides of the antisense strand base pair with the nucleotide sequence of HCV RNA or a portion thereof. The siNA molecule according to claim 1, wherein the 5 'end of the antisense strand may optionally contain a phosphate group. The siNA molecule of claim 1, wherein the nucleotide sequence of the antisense strand or part thereof is complementary to the nucleotide sequence of the 5'-untranslated region of HCV RNA or part thereof. 2. The siNA molecule of claim 1, wherein the nucleotide sequence of the antisense strand or part thereof is complementary to the nucleotide sequence of HCV RNA or part thereof present in the RNA of all HCV isolates. A pharmaceutical composition comprising the siNA molecule of claim 1 in an acceptable carrier or diluent. A pharmaceutical comprising the siNA molecule of claim 1. An active ingredient comprising the siNA molecule of claim 1. Use of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits replication of hepatitis C virus (HCV), wherein one of the strands of the double-stranded siNA molecule is a nucleotide sequence of HCV RNA or a part thereof And the other strand is a sense strand containing a nucleotide sequence complementary to the nucleotide sequence of the antisense strand and is the largest of the pyrimidine nucleotides present in the double stranded siNA molecule. Use wherein the moiety comprises a sugar modification.

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